--- _id: '14408' abstract: - lang: eng text: "We prove that the mesoscopic linear statistics ∑if(na(σi−z0)) of the eigenvalues {σi}i of large n×n non-Hermitian random matrices with complex centred i.i.d. entries are asymptotically Gaussian for any H20-functions f around any point z0 in the bulk of the spectrum on any mesoscopic scale 0Probability Theory and Related Fields. 2023. doi:10.1007/s00440-023-01229-1 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Mesoscopic central limit theorem for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01229-1 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Mesoscopic Central Limit Theorem for Non-Hermitian Random Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-023-01229-1. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Mesoscopic central limit theorem for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2023. ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Mesoscopic central limit theorem for non-Hermitian random matrices. Probability Theory and Related Fields. mla: Cipolloni, Giorgio, et al. “Mesoscopic Central Limit Theorem for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2023, doi:10.1007/s00440-023-01229-1. short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2023). date_created: 2023-10-08T22:01:17Z date_published: 2023-09-28T00:00:00Z date_updated: 2023-10-09T07:19:01Z day: '28' department: - _id: LaEr doi: 10.1007/s00440-023-01229-1 external_id: arxiv: - '2210.12060' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2210.12060 month: '09' oa: 1 oa_version: Preprint publication: Probability Theory and Related Fields publication_identifier: eissn: - 1432-2064 issn: - 0178-8051 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mesoscopic central limit theorem for non-Hermitian random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14417' abstract: - lang: eng text: Entropic risk (ERisk) is an established risk measure in finance, quantifying risk by an exponential re-weighting of rewards. We study ERisk for the first time in the context of turn-based stochastic games with the total reward objective. This gives rise to an objective function that demands the control of systems in a risk-averse manner. We show that the resulting games are determined and, in particular, admit optimal memoryless deterministic strategies. This contrasts risk measures that previously have been considered in the special case of Markov decision processes and that require randomization and/or memory. We provide several results on the decidability and the computational complexity of the threshold problem, i.e. whether the optimal value of ERisk exceeds a given threshold. In the most general case, the problem is decidable subject to Shanuel’s conjecture. If all inputs are rational, the resulting threshold problem can be solved using algebraic numbers, leading to decidability via a polynomial-time reduction to the existential theory of the reals. Further restrictions on the encoding of the input allow the solution of the threshold problem in NP∩coNP. Finally, an approximation algorithm for the optimal value of ERisk is provided. acknowledgement: "This work was partly funded by the ERC CoG 863818 (ForM-SMArt), the DFG Grant\r\n389792660 as part of TRR 248 (Foundations of Perspicuous Software Systems), the Cluster of\r\nExcellence EXC 2050/1 (CeTI, project ID 390696704, as part of Germany’s Excellence Strategy), and the DFG projects BA-1679/11-1 and BA-1679/12-1." alternative_title: - LIPIcs article_number: '15' article_processing_charge: Yes author: - first_name: Christel full_name: Baier, Christel last_name: Baier - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 - first_name: Jakob full_name: Piribauer, Jakob last_name: Piribauer citation: ama: 'Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based stochastic games. In: 48th International Symposium on Mathematical Foundations of Computer Science. Vol 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.MFCS.2023.15' apa: 'Baier, C., Chatterjee, K., Meggendorfer, T., & Piribauer, J. (2023). Entropic risk for turn-based stochastic games. In 48th International Symposium on Mathematical Foundations of Computer Science (Vol. 272). Bordeaux, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2023.15' chicago: Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” In 48th International Symposium on Mathematical Foundations of Computer Science, Vol. 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.MFCS.2023.15. ieee: C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk for turn-based stochastic games,” in 48th International Symposium on Mathematical Foundations of Computer Science, Bordeaux, France, 2023, vol. 272. ista: 'Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2023. Entropic risk for turn-based stochastic games. 48th International Symposium on Mathematical Foundations of Computer Science. MFCS: Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 272, 15.' mla: Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” 48th International Symposium on Mathematical Foundations of Computer Science, vol. 272, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.MFCS.2023.15. short: C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, in:, 48th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. conference: end_date: 2023-09-01 location: Bordeaux, France name: 'MFCS: Symposium on Mathematical Foundations of Computer Science' start_date: 2023-08-28 date_created: 2023-10-09T09:21:05Z date_published: 2023-08-21T00:00:00Z date_updated: 2023-10-09T09:22:37Z day: '21' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPIcs.MFCS.2023.15 ec_funded: 1 external_id: arxiv: - '2307.06611' file: - access_level: open_access checksum: 402281b17ed669bbf149d0fdf68ac201 content_type: application/pdf creator: dernst date_created: 2023-10-09T09:19:11Z date_updated: 2023-10-09T09:19:11Z file_id: '14418' file_name: 2023_LIPIcsMFCS_Baier.pdf file_size: 826843 relation: main_file success: 1 file_date_updated: 2023-10-09T09:19:11Z has_accepted_license: '1' intvolume: ' 272' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: 48th International Symposium on Mathematical Foundations of Computer Science publication_identifier: eissn: - 1868-8969 isbn: - '9783959772921' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Entropic risk for turn-based stochastic games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 272 year: '2023' ... --- _id: '12960' abstract: - lang: eng text: "Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e., submanifolds of Rd defined as the zero set of some multivariate multivalued smooth function f:Rd→Rd−n, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M=f−1(0) is to consider its piecewise linear (PL) approximation M^\r\n based on a triangulation T of the ambient space Rd. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ=1/D (and unavoidably exponential in n). Since it is known that for δ=Ω(d2.5), M^ is O(D2)-close and isotopic to M\r\n, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M^ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. " acknowledgement: The authors have received funding from the European Research Council under the European Union's ERC grant greement 339025 GUDHI (Algorithmic Foundations of Geometric Un-derstanding in Higher Dimensions). The first author was supported by the French government,through the 3IA C\^ote d'Azur Investments in the Future project managed by the National ResearchAgency (ANR) with the reference ANR-19-P3IA-0002. The third author was supported by the Eu-ropean Union's Horizon 2020 research and innovation programme under the Marie Sk\lodowska-Curiegrant agreement 754411 and the FWF (Austrian Science Fund) grant M 3073. article_processing_charge: No article_type: original author: - first_name: Jean Daniel full_name: Boissonnat, Jean Daniel last_name: Boissonnat - first_name: Siargey full_name: Kachanovich, Siargey last_name: Kachanovich - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Boissonnat JD, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 2023;52(2):452-486. doi:10.1137/21M1412918 apa: Boissonnat, J. D., Kachanovich, S., & Wintraecken, M. (2023). Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1412918 chicago: Boissonnat, Jean Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/21M1412918. ieee: J. D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations,” SIAM Journal on Computing, vol. 52, no. 2. Society for Industrial and Applied Mathematics, pp. 452–486, 2023. ista: Boissonnat JD, Kachanovich S, Wintraecken M. 2023. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 52(2), 452–486. mla: Boissonnat, Jean Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” SIAM Journal on Computing, vol. 52, no. 2, Society for Industrial and Applied Mathematics, 2023, pp. 452–86, doi:10.1137/21M1412918. short: J.D. Boissonnat, S. Kachanovich, M. Wintraecken, SIAM Journal on Computing 52 (2023) 452–486. date_created: 2023-05-14T22:01:00Z date_published: 2023-04-30T00:00:00Z date_updated: 2023-10-10T07:34:35Z day: '30' department: - _id: HeEd doi: 10.1137/21M1412918 ec_funded: 1 external_id: isi: - '001013183000012' intvolume: ' 52' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://hal-emse.ccsd.cnrs.fr/3IA-COTEDAZUR/hal-04083489v1 month: '04' oa: 1 oa_version: Submitted Version page: 452-486 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc390959-9c52-11eb-aca3-afa58bd282b2 grant_number: M03073 name: Learning and triangulating manifolds via collapses publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '9441' relation: earlier_version status: public scopus_import: '1' status: public title: Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2023' ... --- _id: '13216' abstract: - lang: eng text: Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude. acknowledgement: "B.C. acknowledges resources provided by the Cambridge Tier2 system operated by the University of Cambridge Research\r\nComputing Service funded by EPSRC Tier-2 capital grant EP/\r\nP020259/1." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Rhys full_name: Bunting, Rhys id: 91deeae8-1207-11ec-b130-c194ad5b50c6 last_name: Bunting orcid: 0000-0001-6928-074X - first_name: Felix full_name: Wodaczek, Felix id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e last_name: Wodaczek orcid: 0009-0000-1457-795X - first_name: Tina full_name: Torabi, Tina last_name: Torabi - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: 'Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 2023;145(27):14894-14902. doi:10.1021/jacs.3c04030' apa: 'Bunting, R., Wodaczek, F., Torabi, T., & Cheng, B. (2023). Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c04030' chicago: 'Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c04030.' ieee: 'R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane,” Journal of the American Chemical Society, vol. 145, no. 27. American Chemical Society, pp. 14894–14902, 2023.' ista: 'Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 145(27), 14894–14902.' mla: 'Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” Journal of the American Chemical Society, vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:10.1021/jacs.3c04030.' short: R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902. date_created: 2023-07-12T09:16:40Z date_published: 2023-06-30T00:00:00Z date_updated: 2023-10-11T08:45:10Z day: '30' ddc: - '540' department: - _id: MaIb - _id: BiCh doi: 10.1021/jacs.3c04030 external_id: isi: - '001020623900001' pmid: - '37390457' file: - access_level: open_access checksum: e07d5323f9c0e5cbd1ad6453f29440ab content_type: application/pdf creator: cchlebak date_created: 2023-07-12T10:22:04Z date_updated: 2023-07-12T10:22:04Z file_id: '13219' file_name: 2023_JACS_Bunting.pdf file_size: 3155843 relation: main_file success: 1 file_date_updated: 2023-07-12T10:22:04Z has_accepted_license: '1' intvolume: ' 145' isi: 1 issue: '27' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 14894-14902 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: 'Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 145 year: '2023' ... --- _id: '14426' abstract: - lang: eng text: To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions, comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion, is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC-to-hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type–specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver. acknowledgement: "We thank the Ober group for discussion and comments on the manuscript. We are grateful to\r\nDr. F. Lemaigre for feedback on the manuscript and Dr. T. Piotrowski for invaluable support.\r\nWe thank the department of experimental medicine (AEM) in Copenhagen for expert fish\r\ncare. We gratefully acknowledge the DanStem Imaging Platform (University of Copenhagen)\r\nfor support and assistance in this work.\r\nThis work is supported by Novo Nordisk Foundation grant NNF17CC0027852 (EAO);\r\nNordisk Foundation grant NNF19OC0058327 (EAO); Novo Nordisk Foundation grant\r\nNNF17OC0031204 (PRL); https://novonordiskfonden.dk/en/; Danish National\r\nResearch Foundation grant DNRF116 (EAO and AT); https://dg.dk/en/; John and Birthe Meyer\r\nFoundation (PRL) and European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement No. 851288 (EH)." article_number: e3002315 article_processing_charge: No article_type: original author: - first_name: Iris A. full_name: Unterweger, Iris A. last_name: Unterweger - first_name: Julie full_name: Klepstad, Julie last_name: Klepstad - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Pia R. full_name: Lundegaard, Pia R. last_name: Lundegaard - first_name: Ala full_name: Trusina, Ala last_name: Trusina - first_name: Elke A. full_name: Ober, Elke A. last_name: Ober citation: ama: Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 2023;21(10). doi:10.1371/journal.pbio.3002315 apa: Unterweger, I. A., Klepstad, J., Hannezo, E. B., Lundegaard, P. R., Trusina, A., & Ober, E. A. (2023). Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002315 chicago: Unterweger, Iris A., Julie Klepstad, Edouard B Hannezo, Pia R. Lundegaard, Ala Trusina, and Elke A. Ober. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002315. ieee: I. A. Unterweger, J. Klepstad, E. B. Hannezo, P. R. Lundegaard, A. Trusina, and E. A. Ober, “Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics,” PLoS Biology, vol. 21, no. 10. Public Library of Science, 2023. ista: Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. 2023. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 21(10), e3002315. mla: Unterweger, Iris A., et al. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” PLoS Biology, vol. 21, no. 10, e3002315, Public Library of Science, 2023, doi:10.1371/journal.pbio.3002315. short: I.A. Unterweger, J. Klepstad, E.B. Hannezo, P.R. Lundegaard, A. Trusina, E.A. Ober, PLoS Biology 21 (2023). date_created: 2023-10-15T22:01:10Z date_published: 2023-10-04T00:00:00Z date_updated: 2023-10-16T07:25:48Z day: '04' ddc: - '570' department: - _id: EdHa doi: 10.1371/journal.pbio.3002315 ec_funded: 1 file: - access_level: open_access checksum: 40a2b11b41d70a0e5939f8a52b66e389 content_type: application/pdf creator: dernst date_created: 2023-10-16T07:20:49Z date_updated: 2023-10-16T07:20:49Z file_id: '14431' file_name: 2023_PloSBiology_Unterweger.pdf file_size: 6193110 relation: main_file success: 1 file_date_updated: 2023-10-16T07:20:49Z has_accepted_license: '1' intvolume: ' 21' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: PLoS Biology publication_identifier: eissn: - 1545-7885 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://github.com/JulieKlepstad/LiverDevelopment scopus_import: '1' status: public title: Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2023' ... --- _id: '14428' abstract: - lang: eng text: "Suppose we have two hash functions h1 and h2, but we trust the security of only one of them. To mitigate this worry, we wish to build a hash combiner Ch1,h2 which is secure so long as one of the underlying hash functions is. This question has been well-studied in the regime of collision resistance. In this case, concatenating the two hash function outputs clearly works. Unfortunately, a long series of works (Boneh and Boyen, CRYPTO’06; Pietrzak, Eurocrypt’07; Pietrzak, CRYPTO’08) showed no (noticeably) shorter combiner for collision resistance is possible.\r\nIn this work, we revisit this pessimistic state of affairs, motivated by the observation that collision-resistance is insufficient for many interesting applications of cryptographic hash functions anyway. We argue the right formulation of the “hash combiner” is to build what we call random oracle (RO) combiners, utilizing stronger assumptions for stronger constructions.\r\nIndeed, we circumvent the previous lower bounds for collision resistance by constructing a simple length-preserving RO combiner C˜h1,h2Z1,Z2(M)=h1(M,Z1)⊕h2(M,Z2),where Z1,Z2\r\n are random salts of appropriate length. We show that this extra randomness is necessary for RO combiners, and indeed our construction is somewhat tight with this lower bound.\r\nOn the negative side, we show that one cannot generically apply the composition theorem to further replace “monolithic” hash functions h1 and h2 by some simpler indifferentiable construction (such as the Merkle-Damgård transformation) from smaller components, such as fixed-length compression functions. Finally, despite this issue, we directly prove collision resistance of the Merkle-Damgård variant of our combiner, where h1 and h2 are replaced by iterative Merkle-Damgård hashes applied to a fixed-length compression function. Thus, we can still subvert the concatenation barrier for collision-resistance combiners while utilizing practically small fixed-length components underneath." alternative_title: - LNCS article_processing_charge: No author: - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Niels full_name: Ferguson, Niels last_name: Ferguson - first_name: Eli full_name: Goldin, Eli last_name: Goldin - first_name: Peter full_name: Hall, Peter last_name: Hall - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. Random oracle combiners: Breaking the concatenation barrier for collision-resistance. In: 43rd Annual International Cryptology Conference. Vol 14082. Springer Nature; 2023:514-546. doi:10.1007/978-3-031-38545-2_17' apa: 'Dodis, Y., Ferguson, N., Goldin, E., Hall, P., & Pietrzak, K. Z. (2023). Random oracle combiners: Breaking the concatenation barrier for collision-resistance. In 43rd Annual International Cryptology Conference (Vol. 14082, pp. 514–546). Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-38545-2_17' chicago: 'Dodis, Yevgeniy, Niels Ferguson, Eli Goldin, Peter Hall, and Krzysztof Z Pietrzak. “Random Oracle Combiners: Breaking the Concatenation Barrier for Collision-Resistance.” In 43rd Annual International Cryptology Conference, 14082:514–46. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-38545-2_17.' ieee: 'Y. Dodis, N. Ferguson, E. Goldin, P. Hall, and K. Z. Pietrzak, “Random oracle combiners: Breaking the concatenation barrier for collision-resistance,” in 43rd Annual International Cryptology Conference, Santa Barbara, CA, United States, 2023, vol. 14082, pp. 514–546.' ista: 'Dodis Y, Ferguson N, Goldin E, Hall P, Pietrzak KZ. 2023. Random oracle combiners: Breaking the concatenation barrier for collision-resistance. 43rd Annual International Cryptology Conference. CRYPTO: Advances in Cryptology, LNCS, vol. 14082, 514–546.' mla: 'Dodis, Yevgeniy, et al. “Random Oracle Combiners: Breaking the Concatenation Barrier for Collision-Resistance.” 43rd Annual International Cryptology Conference, vol. 14082, Springer Nature, 2023, pp. 514–46, doi:10.1007/978-3-031-38545-2_17.' short: Y. Dodis, N. Ferguson, E. Goldin, P. Hall, K.Z. Pietrzak, in:, 43rd Annual International Cryptology Conference, Springer Nature, 2023, pp. 514–546. conference: end_date: 2023-08-24 location: Santa Barbara, CA, United States name: 'CRYPTO: Advances in Cryptology' start_date: 2023-08-20 date_created: 2023-10-15T22:01:11Z date_published: 2023-08-09T00:00:00Z date_updated: 2023-10-16T08:02:11Z day: '09' department: - _id: KrPi doi: 10.1007/978-3-031-38545-2_17 intvolume: ' 14082' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/1041 month: '08' oa: 1 oa_version: Preprint page: 514-546 publication: 43rd Annual International Cryptology Conference publication_identifier: eissn: - 1611-3349 isbn: - '9783031385445' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Random oracle combiners: Breaking the concatenation barrier for collision-resistance' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14082 year: '2023' ... --- _id: '12406' abstract: - lang: eng text: Let X be a sufficiently large positive integer. We prove that one may choose a subset S of primes with cardinality O(logX) such that a positive proportion of integers less than X can be represented by x2+py2 for at least one p∈S. acknowledgement: "This article is a version the author’s master thesis at the University of Bonn. The author would like to thank his advisor Valentin Blomer for introducing the problem, and giving generous feedback and encouragement along the way, especially during the global pandemic.\r\nThe author thanks Edgar Assing for his lectures on analytic number theory. Finally, the author is grateful to the anonymous referees for their valuable time and comments.\r\n" article_processing_charge: No article_type: original author: - first_name: Yijie full_name: Diao, Yijie id: 7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b last_name: Diao orcid: 0000-0002-4989-5330 citation: ama: Diao Y. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 2023;207:1-17. doi:10.4064/aa210830-24-11 apa: Diao, Y. (2023). Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. Instytut Matematyczny. https://doi.org/10.4064/aa210830-24-11 chicago: Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” Acta Arithmetica. Instytut Matematyczny, 2023. https://doi.org/10.4064/aa210830-24-11. ieee: Y. Diao, “Density of the union of positive diagonal binary quadratic forms,” Acta Arithmetica, vol. 207. Instytut Matematyczny, pp. 1–17, 2023. ista: Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 207, 1–17. mla: Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” Acta Arithmetica, vol. 207, Instytut Matematyczny, 2023, pp. 1–17, doi:10.4064/aa210830-24-11. short: Y. Diao, Acta Arithmetica 207 (2023) 1–17. date_created: 2023-01-26T21:17:04Z date_published: 2023-01-09T00:00:00Z date_updated: 2023-10-17T09:15:17Z day: '09' department: - _id: GradSch doi: 10.4064/aa210830-24-11 external_id: arxiv: - '2103.08268' isi: - '000912903000001' intvolume: ' 207' isi: 1 keyword: - Algebra - Number Theory language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2103.08268 month: '01' oa: 1 oa_version: Preprint page: 1-17 publication: Acta Arithmetica publication_identifier: eissn: - 1730-6264 issn: - 0065-1036 publication_status: published publisher: Instytut Matematyczny quality_controlled: '1' status: public title: Density of the union of positive diagonal binary quadratic forms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 207 year: '2023' ... --- _id: '13200' abstract: - lang: eng text: Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks. acknowledgement: This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. article_number: '3784' article_processing_charge: No article_type: original author: - first_name: Liu full_name: Qiu, Liu id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac last_name: Qiu orcid: 0000-0003-4345-4267 - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 2023;14. doi:10.1038/s41467-023-39493-3 apa: Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., & Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-023-39493-3 chicago: Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications. Nature Research, 2023. https://doi.org/10.1038/s41467-023-39493-3. ieee: L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” Nature Communications, vol. 14. Nature Research, 2023. ista: Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784. mla: Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications, vol. 14, 3784, Nature Research, 2023, doi:10.1038/s41467-023-39493-3. short: L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023). date_created: 2023-07-09T22:01:11Z date_published: 2023-06-24T00:00:00Z date_updated: 2023-10-17T11:46:12Z day: '24' ddc: - '000' department: - _id: JoFi doi: 10.1038/s41467-023-39493-3 ec_funded: 1 external_id: arxiv: - '2210.12443' isi: - '001018100800002' pmid: - '37355691' file: - access_level: open_access checksum: ec7ccd2c08f90d59cab302fd0d7776a4 content_type: application/pdf creator: alisjak date_created: 2023-07-10T10:10:54Z date_updated: 2023-07-10T10:10:54Z file_id: '13206' file_name: 2023_NatureComms_Qiu.pdf file_size: 1349134 relation: main_file success: 1 file_date_updated: 2023-07-10T10:10:54Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2671EB66-B435-11E9-9278-68D0E5697425 name: Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Nature Research quality_controlled: '1' scopus_import: '1' status: public title: Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '13315' abstract: - lang: eng text: How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties. acknowledgement: J.B. was funded by the European Union (ERC, CHORAL, project number 101039794). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank the reviewers for the insightful comments and, in particular, for suggesting the BAMP-inspired denoisers leading to AMP-AP. article_number: e2302028120 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jean full_name: Barbier, Jean last_name: Barbier - first_name: Francesco full_name: Camilli, Francesco last_name: Camilli - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Manuel full_name: Sáenz, Manuel last_name: Sáenz citation: ama: Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(30). doi:10.1073/pnas.2302028120 apa: Barbier, J., Camilli, F., Mondelli, M., & Sáenz, M. (2023). Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2302028120 chicago: Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2302028120. ieee: J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in structured principal component analysis and how to reach them,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30. National Academy of Sciences, 2023. ista: Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 120(30), e2302028120. mla: Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 30, e2302028120, National Academy of Sciences, 2023, doi:10.1073/pnas.2302028120. short: J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023). date_created: 2023-07-30T22:01:02Z date_published: 2023-07-25T00:00:00Z date_updated: 2023-10-17T11:44:55Z day: '25' ddc: - '000' department: - _id: MaMo doi: 10.1073/pnas.2302028120 external_id: pmid: - '37463204' file: - access_level: open_access checksum: 1fc06228afdb3aa80cf8e7766bcf9dc5 content_type: application/pdf creator: dernst date_created: 2023-07-31T07:30:48Z date_updated: 2023-07-31T07:30:48Z file_id: '13323' file_name: 2023_PNAS_Barbier.pdf file_size: 995933 relation: main_file success: 1 file_date_updated: 2023-07-31T07:30:48Z has_accepted_license: '1' intvolume: ' 120' issue: '30' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/fcamilli95/Structured-PCA- scopus_import: '1' status: public title: Fundamental limits in structured principal component analysis and how to reach them tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 120 year: '2023' ... --- _id: '14037' abstract: - lang: eng text: 'Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions.' acknowledgement: N.M.-S. acknowledges the support of the Ministry of Energy, Israel, as part of the scholarship program for graduate students in the fields of energy. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation, Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support of the BSF-NSF 094 Grant No. 2022503. article_number: e2300828120 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ofek full_name: Vardi, Ofek last_name: Vardi - first_name: Naama full_name: Maroudas-Sklare, Naama last_name: Maroudas-Sklare - first_name: Yuval full_name: Kolodny, Yuval last_name: Kolodny - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Amijai full_name: Saragovi, Amijai last_name: Saragovi - first_name: Nir full_name: Galili, Nir last_name: Galili - first_name: Stav full_name: Ferrera, Stav last_name: Ferrera - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Nir full_name: Yuran, Nir last_name: Yuran - first_name: Hagit P. full_name: Affek, Hagit P. last_name: Affek - first_name: Boaz full_name: Luz, Boaz last_name: Luz - first_name: Yonaton full_name: Goldsmith, Yonaton last_name: Goldsmith - first_name: Nir full_name: Keren, Nir last_name: Keren - first_name: Shira full_name: Yochelis, Shira last_name: Yochelis - first_name: Itay full_name: Halevy, Itay last_name: Halevy - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Yossi full_name: Paltiel, Yossi last_name: Paltiel citation: ama: Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(32). doi:10.1073/pnas.2300828120 apa: Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili, N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2300828120 chicago: Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2300828120. ieee: O. Vardi et al., “Nuclear spin effects in biological processes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 32. National Academy of Sciences, 2023. ista: Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N, Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes. Proceedings of the National Academy of Sciences of the United States of America. 120(32), e2300828120. mla: Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:10.1073/pnas.2300828120. short: O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili, S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren, S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy of Sciences of the United States of America 120 (2023). date_created: 2023-08-13T22:01:12Z date_published: 2023-07-31T00:00:00Z date_updated: 2023-10-17T11:45:25Z day: '31' ddc: - '530' department: - _id: MiLe doi: 10.1073/pnas.2300828120 ec_funded: 1 external_id: pmid: - '37523549' file: - access_level: open_access checksum: a5ed64788a5acef9b9a300a26fa5a177 content_type: application/pdf creator: dernst date_created: 2023-08-14T07:43:45Z date_updated: 2023-08-14T07:43:45Z file_id: '14047' file_name: 2023_PNAS_Vardi.pdf file_size: 1003092 relation: main_file success: 1 file_date_updated: 2023-08-14T07:43:45Z has_accepted_license: '1' intvolume: ' 120' issue: '32' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Nuclear spin effects in biological processes tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 120 year: '2023' ... --- _id: '12683' abstract: - lang: eng text: We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices. acknowledgement: G. Dubach gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. L. Erdős is supported by ERC Advanced Grant “RMTBeyond” No. 101020331. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Dubach, Guillaume id: D5C6A458-10C4-11EA-ABF4-A4B43DDC885E last_name: Dubach orcid: 0000-0001-6892-8137 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Dubach G, Erdös L. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 2023;28:1-13. doi:10.1214/23-ECP516 apa: Dubach, G., & Erdös, L. (2023). Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-ECP516 chicago: Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP516. ieee: G. Dubach and L. Erdös, “Dynamics of a rank-one perturbation of a Hermitian matrix,” Electronic Communications in Probability, vol. 28. Institute of Mathematical Statistics, pp. 1–13, 2023. ista: Dubach G, Erdös L. 2023. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 28, 1–13. mla: Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” Electronic Communications in Probability, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–13, doi:10.1214/23-ECP516. short: G. Dubach, L. Erdös, Electronic Communications in Probability 28 (2023) 1–13. date_created: 2023-02-26T23:01:01Z date_published: 2023-02-08T00:00:00Z date_updated: 2023-10-17T12:48:10Z day: '08' ddc: - '510' department: - _id: LaEr doi: 10.1214/23-ECP516 ec_funded: 1 external_id: arxiv: - '2108.13694' isi: - '000950650200005' file: - access_level: open_access checksum: a1c6f0a3e33688fd71309c86a9aad86e content_type: application/pdf creator: dernst date_created: 2023-02-27T09:43:27Z date_updated: 2023-02-27T09:43:27Z file_id: '12692' file_name: 2023_ElectCommProbability_Dubach.pdf file_size: 479105 relation: main_file success: 1 file_date_updated: 2023-02-27T09:43:27Z has_accepted_license: '1' intvolume: ' 28' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1-13 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Electronic Communications in Probability publication_identifier: eissn: - 1083-589X publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Dynamics of a rank-one perturbation of a Hermitian matrix tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2023' ... --- _id: '12761' abstract: - lang: eng text: "We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine\r\nthe fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent\r\nmultiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048)." acknowledgement: The second author is partially funded by the ERC Advanced Grant “RMTBEYOND” No. 101020331. The third author is supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation. article_processing_charge: No article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 2023;33(1):447-489. doi:10.1214/22-AAP1820 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Functional central limit theorems for Wigner matrices. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AAP1820 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Functional Central Limit Theorems for Wigner Matrices.” Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AAP1820. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Functional central limit theorems for Wigner matrices,” Annals of Applied Probability, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 447–489, 2023. ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 33(1), 447–489. mla: Cipolloni, Giorgio, et al. “Functional Central Limit Theorems for Wigner Matrices.” Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 447–89, doi:10.1214/22-AAP1820. short: G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023) 447–489. date_created: 2023-03-26T22:01:08Z date_published: 2023-02-01T00:00:00Z date_updated: 2023-10-17T12:48:52Z day: '01' department: - _id: LaEr doi: 10.1214/22-AAP1820 ec_funded: 1 external_id: arxiv: - '2012.13218' isi: - '000946432400015' intvolume: ' 33' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.13218 month: '02' oa: 1 oa_version: Preprint page: 447-489 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Annals of Applied Probability publication_identifier: issn: - 1050-5164 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Functional central limit theorems for Wigner matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2023' ... --- _id: '8682' abstract: - lang: eng text: It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces. article_processing_charge: No article_type: original author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Pierre Le full_name: Boudec, Pierre Le last_name: Boudec - first_name: Will full_name: Sawin, Will last_name: Sawin citation: ama: Browning TD, Boudec PL, Sawin W. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 2023;197(3):1115-1203. doi:10.4007/annals.2023.197.3.3 apa: Browning, T. D., Boudec, P. L., & Sawin, W. (2023). The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. Princeton University. https://doi.org/10.4007/annals.2023.197.3.3 chicago: Browning, Timothy D, Pierre Le Boudec, and Will Sawin. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics. Princeton University, 2023. https://doi.org/10.4007/annals.2023.197.3.3. ieee: T. D. Browning, P. L. Boudec, and W. Sawin, “The Hasse principle for random Fano hypersurfaces,” Annals of Mathematics, vol. 197, no. 3. Princeton University, pp. 1115–1203, 2023. ista: Browning TD, Boudec PL, Sawin W. 2023. The Hasse principle for random Fano hypersurfaces. Annals of Mathematics. 197(3), 1115–1203. mla: Browning, Timothy D., et al. “The Hasse Principle for Random Fano Hypersurfaces.” Annals of Mathematics, vol. 197, no. 3, Princeton University, 2023, pp. 1115–203, doi:10.4007/annals.2023.197.3.3. short: T.D. Browning, P.L. Boudec, W. Sawin, Annals of Mathematics 197 (2023) 1115–1203. date_created: 2020-10-19T14:28:50Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-10-17T12:47:43Z day: '01' department: - _id: TiBr doi: 10.4007/annals.2023.197.3.3 external_id: arxiv: - '2006.02356' isi: - '000966611000003' intvolume: ' 197' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2006.02356 month: '05' oa: 1 oa_version: Preprint page: 1115-1203 publication: Annals of Mathematics publication_identifier: issn: - 0003-486X publication_status: published publisher: Princeton University quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/when-is-necessary-sufficient/ status: public title: The Hasse principle for random Fano hypersurfaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 197 year: '2023' ... --- _id: '12706' abstract: - lang: eng text: Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude. acknowledgement: "This research was supported by an Australian Government Research Training Program\r\n(RTP) Scholarship to JCM (https://www.dese.gov.au), and LB is supported by the Centre de\r\nrecherche sur le vieillissement Fellowship Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." article_processing_charge: No article_type: original author: - first_name: Jody C. full_name: Mckerral, Jody C. last_name: Mckerral - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina - first_name: Vladimir full_name: Ejov, Vladimir last_name: Ejov - first_name: Louise full_name: Bartle, Louise last_name: Bartle - first_name: James G. full_name: Mitchell, James G. last_name: Mitchell - first_name: Jerzy A. full_name: Filar, Jerzy A. last_name: Filar citation: ama: Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 2023;18(2):e0279838. doi:10.1371/journal.pone.0279838 apa: Mckerral, J. C., Kleshnina, M., Ejov, V., Bartle, L., Mitchell, J. G., & Filar, J. A. (2023). Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0279838 chicago: Mckerral, Jody C., Maria Kleshnina, Vladimir Ejov, Louise Bartle, James G. Mitchell, and Jerzy A. Filar. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” PLoS One. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0279838. ieee: J. C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J. G. Mitchell, and J. A. Filar, “Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations,” PLoS One, vol. 18, no. 2. Public Library of Science, p. e0279838, 2023. ista: Mckerral JC, Kleshnina M, Ejov V, Bartle L, Mitchell JG, Filar JA. 2023. Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations. PLoS One. 18(2), e0279838. mla: Mckerral, Jody C., et al. “Empirical Parameterisation and Dynamical Analysis of the Allometric Rosenzweig-MacArthur Equations.” PLoS One, vol. 18, no. 2, Public Library of Science, 2023, p. e0279838, doi:10.1371/journal.pone.0279838. short: J.C. Mckerral, M. Kleshnina, V. Ejov, L. Bartle, J.G. Mitchell, J.A. Filar, PLoS One 18 (2023) e0279838. date_created: 2023-03-05T23:01:05Z date_published: 2023-02-27T00:00:00Z date_updated: 2023-10-17T12:53:30Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pone.0279838 external_id: isi: - '000996122900022' pmid: - '36848357' file: - access_level: open_access checksum: 798ed5739a4117b03173e5d56e0534c9 content_type: application/pdf creator: cchlebak date_created: 2023-03-07T10:26:45Z date_updated: 2023-03-07T10:26:45Z file_id: '12712' file_name: 2023_PLOSOne_Mckerral.pdf file_size: 1257003 relation: main_file success: 1 file_date_updated: 2023-03-07T10:26:45Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: e0279838 pmid: 1 publication: PLoS One publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2023' ... --- _id: '13202' abstract: - lang: eng text: Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons. acknowledged_ssus: - _id: EM-Fac acknowledgement: This work was supported by The Institute of Science and Technology (IST) Austria, the European Union's Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 793482 (to K.E.) and by the European Research Council (ERC) Grant Agreement No. 694539 (to R.S.). We thank Nicoleta Condruz (IST Austria, Klosterneuburg, Austria) for technical assistance with sample preparation, the Electron Microscopy Facility of IST Austria (Klosterneuburg, Austria) for technical support with EM works, Natalia Baranova (University of Vienna, Vienna, Austria) and Martin Loose (IST Austria, Klosterneuburg, Austria) for advice on liposome preparation, and Yugo Fukazawa (University of Fukui, Fukui, Japan) for comments. article_processing_charge: No article_type: original author: - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Elodie full_name: Le Monnier, Elodie id: 3B59276A-F248-11E8-B48F-1D18A9856A87 last_name: Le Monnier - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Eguchi K, Le Monnier E, Shigemoto R. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 2023;43(23):4197-4216. doi:10.1523/JNEUROSCI.1514-22.2023 apa: Eguchi, K., Le Monnier, E., & Shigemoto, R. (2023). Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1514-22.2023 chicago: Eguchi, Kohgaku, Elodie Le Monnier, and Ryuichi Shigemoto. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.1514-22.2023. ieee: K. Eguchi, E. Le Monnier, and R. Shigemoto, “Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons,” The Journal of Neuroscience, vol. 43, no. 23. Society for Neuroscience, pp. 4197–4216, 2023. ista: Eguchi K, Le Monnier E, Shigemoto R. 2023. Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons. The Journal of Neuroscience. 43(23), 4197–4216. mla: Eguchi, Kohgaku, et al. “Nanoscale Phosphoinositide Distribution on Cell Membranes of Mouse Cerebellar Neurons.” The Journal of Neuroscience, vol. 43, no. 23, Society for Neuroscience, 2023, pp. 4197–216, doi:10.1523/JNEUROSCI.1514-22.2023. short: K. Eguchi, E. Le Monnier, R. Shigemoto, The Journal of Neuroscience 43 (2023) 4197–4216. date_created: 2023-07-09T22:01:12Z date_published: 2023-06-07T00:00:00Z date_updated: 2023-10-18T07:12:47Z day: '07' ddc: - '570' department: - _id: RySh doi: 10.1523/JNEUROSCI.1514-22.2023 ec_funded: 1 external_id: isi: - '001020132100005' pmid: - '37160366' file: - access_level: open_access checksum: 70b2141870e0bf1c94fd343e18fdbc32 content_type: application/pdf creator: alisjak date_created: 2023-07-10T09:04:58Z date_updated: 2023-07-10T09:04:58Z file_id: '13205' file_name: 2023_JN_Eguchi.pdf file_size: 7794425 relation: main_file success: 1 file_date_updated: 2023-07-10T09:04:58Z has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '23' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 4197-4216 pmid: 1 project: - _id: 2659CC84-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '793482' name: 'Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission' - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' publication: The Journal of Neuroscience publication_identifier: eissn: - 1529-2401 issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2023' ... --- _id: '12916' abstract: - lang: eng text: "We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface.\r\n" article_processing_charge: No article_type: original author: - first_name: Dante full_name: Bonolis, Dante id: 6A459894-5FDD-11E9-AF35-BB24E6697425 last_name: Bonolis - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 2023;24(1):173-204. doi:10.2422/2036-2145.202010_018 apa: Bonolis, D., & Browning, T. D. (2023). Uniform bounds for rational points on hyperelliptic fibrations. Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale. https://doi.org/10.2422/2036-2145.202010_018 chicago: Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze. Scuola Normale Superiore - Edizioni della Normale, 2023. https://doi.org/10.2422/2036-2145.202010_018. ieee: D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic fibrations,” Annali della Scuola Normale Superiore di Pisa - Classe di Scienze, vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204, 2023. ista: Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 24(1), 173–204. mla: Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della Normale, 2023, pp. 173–204, doi:10.2422/2036-2145.202010_018. short: D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze 24 (2023) 173–204. date_created: 2023-05-07T22:01:04Z date_published: 2023-02-16T00:00:00Z date_updated: 2023-10-18T06:54:30Z day: '16' department: - _id: TiBr doi: 10.2422/2036-2145.202010_018 external_id: arxiv: - '2007.14182' intvolume: ' 24' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2007.14182 month: '02' oa: 1 oa_version: Preprint page: 173-204 publication: Annali della Scuola Normale Superiore di Pisa - Classe di Scienze publication_identifier: eissn: - 2036-2145 issn: - 0391-173X publication_status: published publisher: Scuola Normale Superiore - Edizioni della Normale quality_controlled: '1' scopus_import: '1' status: public title: Uniform bounds for rational points on hyperelliptic fibrations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2023' ... --- _id: '14374' abstract: - lang: eng text: "Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Barbara full_name: Roos, Barbara id: 5DA90512-D80F-11E9-8994-2E2EE6697425 last_name: Roos orcid: 0000-0002-9071-5880 citation: ama: Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374 apa: Roos, B. (2023). Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374 chicago: Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374. ieee: B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023. ista: Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. mla: Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14374. short: B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023. date_created: 2023-09-28T14:23:04Z date_published: 2023-09-30T00:00:00Z date_updated: 2023-10-27T10:37:30Z day: '30' ddc: - '515' - '539' degree_awarded: PhD department: - _id: GradSch - _id: RoSe doi: 10.15479/at:ista:14374 ec_funded: 1 file: - access_level: open_access checksum: ef039ffc3de2cb8dee5b14110938e9b6 content_type: application/pdf creator: broos date_created: 2023-10-06T11:35:56Z date_updated: 2023-10-06T11:35:56Z file_id: '14398' file_name: phd-thesis-draft_pdfa_acrobat.pdf file_size: 2365702 relation: main_file - access_level: closed checksum: 81dcac33daeefaf0111db52f41bb1fd0 content_type: application/x-zip-compressed creator: broos date_created: 2023-10-06T11:38:01Z date_updated: 2023-10-06T11:38:01Z file_id: '14399' file_name: Version5.zip file_size: 4691734 relation: source_file file_date_updated: 2023-10-06T11:38:01Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '09' oa: 1 oa_version: Published Version page: '206' project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13207' relation: part_of_dissertation status: public - id: '10850' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: Boundary superconductivity in BCS theory tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13207' abstract: - lang: eng text: We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity. acknowledgement: We thank Egor Babaev for encouraging us to study this problem, and Rupert Frank for many fruitful discussions. scussions. Funding. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (Barbara Roos and Robert Seiringer) is gratefully acknowledged. article_processing_charge: No article_type: original author: - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Barbara full_name: Roos, Barbara id: 5DA90512-D80F-11E9-8994-2E2EE6697425 last_name: Roos orcid: 0000-0002-9071-5880 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 2023;12(4):1507–1540. doi:10.4171/JST/439 apa: Hainzl, C., Roos, B., & Seiringer, R. (2023). Boundary superconductivity in the BCS model. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/439 chicago: Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/439. ieee: C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS model,” Journal of Spectral Theory, vol. 12, no. 4. EMS Press, pp. 1507–1540, 2023. ista: Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 12(4), 1507–1540. mla: Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:10.4171/JST/439. short: C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540. date_created: 2023-07-10T16:35:45Z date_published: 2023-05-18T00:00:00Z date_updated: 2023-10-27T10:37:29Z day: '18' ddc: - '530' department: - _id: GradSch - _id: RoSe doi: 10.4171/JST/439 ec_funded: 1 external_id: arxiv: - '2201.08090' isi: - '000997933500008' file: - access_level: open_access checksum: 5501da33be010b5c81440438287584d5 content_type: application/pdf creator: alisjak date_created: 2023-07-11T08:19:15Z date_updated: 2023-07-11T08:19:15Z file_id: '13208' file_name: 2023_EMS_Hainzl.pdf file_size: 304619 relation: main_file success: 1 file_date_updated: 2023-07-11T08:19:15Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1507–1540 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Journal of Spectral Theory publication_identifier: eissn: - 1664-0403 issn: - 1664-039X publication_status: published publisher: EMS Press quality_controlled: '1' related_material: record: - id: '14374' relation: dissertation_contains status: public status: public title: Boundary superconductivity in the BCS model tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2023' ... --- _id: '14452' abstract: - lang: eng text: The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√⁠. We illustrate our results with some numerical examples. acknowledgement: NHB was supported in part by ERC Grants 250152 and 101055327. AV was partly supported by the chaire Modélisation Mathématique et Biodiversité of Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation X. article_number: iyad133 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison M. full_name: Etheridge, Alison M. last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics. 2023;225(2). doi:10.1093/genetics/iyad133 apa: Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal model with dominance. Genetics. Oxford Academic. https://doi.org/10.1093/genetics/iyad133 chicago: Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal Model with Dominance.” Genetics. Oxford Academic, 2023. https://doi.org/10.1093/genetics/iyad133. ieee: N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with dominance,” Genetics, vol. 225, no. 2. Oxford Academic, 2023. ista: Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance. Genetics. 225(2), iyad133. mla: Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics, vol. 225, no. 2, iyad133, Oxford Academic, 2023, doi:10.1093/genetics/iyad133. short: N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023). date_created: 2023-10-29T23:01:15Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-10-30T13:04:11Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1093/genetics/iyad133 ec_funded: 1 external_id: arxiv: - '2211.03515' file: - access_level: open_access checksum: 3f65b1fbe813e2f4dbb5d2b5e891844a content_type: application/pdf creator: dernst date_created: 2023-10-30T12:57:53Z date_updated: 2023-10-30T12:57:53Z file_id: '14469' file_name: 2023_Genetics_Barton.pdf file_size: 1439032 relation: main_file success: 1 file_date_updated: 2023-10-30T12:57:53Z has_accepted_license: '1' intvolume: ' 225' issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication: Genetics publication_identifier: eissn: - 1943-2631 issn: - 0016-6731 publication_status: published publisher: Oxford Academic quality_controlled: '1' related_material: record: - id: '12949' relation: research_data status: public scopus_import: '1' status: public title: The infinitesimal model with dominance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 225 year: '2023' ... --- _id: '12949' abstract: - lang: eng text: The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed. article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949 apa: Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949 chicago: Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949. ieee: N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023. ista: Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949. mla: Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949. short: N.H. Barton, (2023). contributor: - contributor_type: researcher first_name: Amandine last_name: Veber - contributor_type: researcher first_name: Alison last_name: Etheridge date_created: 2023-05-13T09:49:09Z date_published: 2023-05-13T00:00:00Z date_updated: 2023-10-30T13:04:11Z day: '13' ddc: - '576' department: - _id: NiBa doi: 10.15479/AT:ISTA:12949 file: - access_level: open_access checksum: b0ce7d4b1ee7e7265430ceed36fc3336 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:36:33Z date_updated: 2023-05-13T09:36:33Z file_id: '12950' file_name: Neutral identities 16th Jan file_size: 13662 relation: main_file success: 1 - access_level: open_access checksum: ad5035ad4f7d3b150a252c79884f6a83 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:38:17Z date_updated: 2023-05-13T09:38:17Z file_id: '12951' file_name: p, zA, zD, N=30 neutral III file_size: 181619928 relation: main_file success: 1 - access_level: open_access checksum: 62182a1de796256edd6f4223704312ef content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:41:59Z date_updated: 2023-05-13T09:41:59Z file_id: '12952' file_name: p, zA, zD, N=30 neutral IV file_size: 605902074 relation: main_file success: 1 - access_level: open_access checksum: af775dda5c4f6859cb1e5a81ec40a667 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:52Z date_updated: 2023-05-13T09:46:52Z file_id: '12953' file_name: p, zA, zD, N=30 selected k=5 file_size: 1018238746 relation: main_file success: 1 - access_level: open_access checksum: af26f3394c387d3ada14b434cd68b1e5 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:42:05Z date_updated: 2023-05-13T09:42:05Z file_id: '12954' file_name: Pairwise F N=30 neutral II file_size: 3197160 relation: main_file success: 1 - access_level: open_access checksum: d5da7dc0e7282dd48222e26d12e34220 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:42:06Z date_updated: 2023-05-13T09:42:06Z file_id: '12955' file_name: Pedigrees N=30 neutral II file_size: 55492 relation: main_file success: 1 - access_level: open_access checksum: 00f386d80677590e29f6235d49cba58d content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:06Z date_updated: 2023-05-13T09:46:06Z file_id: '12956' file_name: selected reps N=30 selected k=1,2 300 reps III file_size: 474003467 relation: main_file success: 1 - access_level: open_access checksum: 658cef3eaea6136a4d24da4f074191d7 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:08Z date_updated: 2023-05-13T09:46:08Z file_id: '12957' file_name: Algorithm for caclulating identities.nb file_size: 121209 relation: main_file success: 1 - access_level: open_access checksum: db9b6dddd7a596d974e25f5e78f5c45c content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:08Z date_updated: 2023-05-13T09:46:08Z file_id: '12958' file_name: Infinitesimal with dominance.nb file_size: 1803898 relation: main_file success: 1 - access_level: open_access checksum: 91f80a9fb58cae8eef2d8bf59fe30189 content_type: text/plain creator: nbarton date_created: 2023-05-16T04:09:08Z date_updated: 2023-05-16T04:09:08Z file_id: '12967' file_name: ReadMe.txt file_size: 990 relation: main_file success: 1 file_date_updated: 2023-05-16T04:09:08Z has_accepted_license: '1' keyword: - Quantitative genetics - infinitesimal model month: '05' oa: 1 oa_version: Published Version project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publisher: Institute of Science and Technology Austria related_material: record: - id: '14452' relation: used_in_publication status: public status: public title: The infinitesimal model with dominance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14461' abstract: - lang: eng text: 'Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model’s weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.' acknowledged_ssus: - _id: ScienComp acknowledgement: The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), as well as experimental support from the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois Schloegl. AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT), the support of Fondation Hadamard with a PRMO grant, and the support of CNRS with a CoopIntEER IEA grant (project ALFRED). alternative_title: - PMLR article_processing_charge: No author: - first_name: Ilia full_name: Markov, Ilia id: D0CF4148-C985-11E9-8066-0BDEE5697425 last_name: Markov - first_name: Adrian full_name: Vladu, Adrian last_name: Vladu - first_name: Qi full_name: Guo, Qi last_name: Guo - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Markov I, Vladu A, Guo Q, Alistarh D-A. Quantized distributed training of large models with convergence guarantees. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:24020-24044.' apa: 'Markov, I., Vladu, A., Guo, Q., & Alistarh, D.-A. (2023). Quantized distributed training of large models with convergence guarantees. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 24020–24044). Honolulu, Hawaii, HI, United States: ML Research Press.' chicago: Markov, Ilia, Adrian Vladu, Qi Guo, and Dan-Adrian Alistarh. “Quantized Distributed Training of Large Models with Convergence Guarantees.” In Proceedings of the 40th International Conference on Machine Learning, 202:24020–44. ML Research Press, 2023. ieee: I. Markov, A. Vladu, Q. Guo, and D.-A. Alistarh, “Quantized distributed training of large models with convergence guarantees,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 24020–24044. ista: 'Markov I, Vladu A, Guo Q, Alistarh D-A. 2023. Quantized distributed training of large models with convergence guarantees. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 24020–24044.' mla: Markov, Ilia, et al. “Quantized Distributed Training of Large Models with Convergence Guarantees.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 24020–44. short: I. Markov, A. Vladu, Q. Guo, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 24020–24044. conference: end_date: 2023-07-29 location: Honolulu, Hawaii, HI, United States name: 'ICML: International Conference on Machine Learning' start_date: 2023-07-23 date_created: 2023-10-29T23:01:17Z date_published: 2023-07-30T00:00:00Z date_updated: 2023-10-31T09:40:45Z day: '30' department: - _id: DaAl ec_funded: 1 external_id: arxiv: - '2302.02390' intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2302.02390 month: '07' oa: 1 oa_version: Preprint page: 24020-24044 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 40th International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Quantized distributed training of large models with convergence guarantees type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '14462' abstract: - lang: eng text: "We study fine-grained error bounds for differentially private algorithms for counting under continual observation. Our main insight is that the matrix mechanism when using lower-triangular matrices can be used in the continual observation model. More specifically, we give an explicit factorization for the counting matrix Mcount and upper bound the error explicitly. We also give a fine-grained analysis, specifying the exact constant in the upper bound. Our analysis is based on upper and lower bounds of the completely bounded norm (cb-norm) of Mcount\r\n. Along the way, we improve the best-known bound of 28 years by Mathias (SIAM Journal on Matrix Analysis and Applications, 1993) on the cb-norm of Mcount for a large range of the dimension of Mcount. Furthermore, we are the first to give concrete error bounds for various problems under continual observation such as binary counting, maintaining a histogram, releasing an approximately cut-preserving synthetic graph, many graph-based statistics, and substring and episode counting. Finally, we note that our result can be used to get a fine-grained error bound for non-interactive local learning and the first lower bounds on the additive error for (ϵ,δ)-differentially-private counting under continual observation. Subsequent to this work, Henzinger et al. (SODA, 2023) showed that our factorization also achieves fine-grained mean-squared error." acknowledgement: "This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project Z 422-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. 2020–2024. JU’s research was funded by Decanal Research Grant. A part of this work was done when JU was visiting Indian Statistical Institute, Delhi. The authors would like to thank Rajat Bhatia, Aleksandar Nikolov, Shanta Laisharam, Vern Paulsen, Ryan Rogers, Abhradeep Thakurta, and Sarvagya Upadhyay for useful discussions." alternative_title: - PMLR article_processing_charge: No author: - first_name: Hendrik full_name: Fichtenberger, Hendrik last_name: Fichtenberger - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Jalaj full_name: Upadhyay, Jalaj last_name: Upadhyay citation: ama: 'Fichtenberger H, Henzinger MH, Upadhyay J. Constant matters: Fine-grained error bound on differentially private continual observation. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:10072-10092.' apa: 'Fichtenberger, H., Henzinger, M. H., & Upadhyay, J. (2023). Constant matters: Fine-grained error bound on differentially private continual observation. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 10072–10092). Honolulu, Hawaii, HI, United States: ML Research Press.' chicago: 'Fichtenberger, Hendrik, Monika H Henzinger, and Jalaj Upadhyay. “Constant Matters: Fine-Grained Error Bound on Differentially Private Continual Observation.” In Proceedings of the 40th International Conference on Machine Learning, 202:10072–92. ML Research Press, 2023.' ieee: 'H. Fichtenberger, M. H. Henzinger, and J. Upadhyay, “Constant matters: Fine-grained error bound on differentially private continual observation,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 10072–10092.' ista: 'Fichtenberger H, Henzinger MH, Upadhyay J. 2023. Constant matters: Fine-grained error bound on differentially private continual observation. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 10072–10092.' mla: 'Fichtenberger, Hendrik, et al. “Constant Matters: Fine-Grained Error Bound on Differentially Private Continual Observation.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10072–92.' short: H. Fichtenberger, M.H. Henzinger, J. Upadhyay, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 10072–10092. conference: end_date: 2023-07-29 location: Honolulu, Hawaii, HI, United States name: 'ICML: International Conference on Machine Learning' start_date: 2023-07-23 date_created: 2023-10-29T23:01:17Z date_published: 2023-07-30T00:00:00Z date_updated: 2023-10-31T09:54:05Z day: '30' department: - _id: MoHe ec_funded: 1 intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.mlr.press/v202/fichtenberger23a/fichtenberger23a.pdf month: '07' oa: 1 oa_version: Published Version page: 10072-10092 project: - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures - _id: 34def286-11ca-11ed-8bc3-da5948e1613c grant_number: Z00422 name: Wittgenstein Award - Monika Henzinger - _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe grant_number: 'P33775 ' name: Fast Algorithms for a Reactive Network Layer publication: Proceedings of the 40th International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: 'Constant matters: Fine-grained error bound on differentially private continual observation' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '14459' abstract: - lang: eng text: Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions. acknowledgement: Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE). alternative_title: - PMLR article_processing_charge: No author: - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko - first_name: Kevin full_name: Kögler, Kevin id: 94ec913c-dc85-11ea-9058-e5051ab2428b last_name: Kögler - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:31151-31209.' apa: 'Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.' chicago: Shevchenko, Aleksandr, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In Proceedings of the 40th International Conference on Machine Learning, 202:31151–209. ML Research Press, 2023. ieee: A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209. ista: 'Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.' mla: Shevchenko, Aleksandr, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209. short: A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209. conference: end_date: 2023-07-29 location: Honolulu, Hawaii, HI, United States name: 'ICML: International Conference on Machine Learning' start_date: 2023-07-23 date_created: 2023-10-29T23:01:17Z date_published: 2023-07-30T00:00:00Z date_updated: 2023-10-31T08:52:28Z day: '30' department: - _id: MaMo - _id: DaAl external_id: arxiv: - '2212.13468' intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2212.13468 month: '07' oa: 1 oa_version: Preprint page: 31151-31209 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the 40th International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Fundamental limits of two-layer autoencoders, and achieving them with gradient methods type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '14460' abstract: - lang: eng text: We provide an efficient implementation of the backpropagation algorithm, specialized to the case where the weights of the neural network being trained are sparse. Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and common layer types (e.g., convolutional or linear). We provide a fast vectorized implementation on commodity CPUs, and show that it can yield speedups in end-to-end runtime experiments, both in transfer learning using already-sparsified networks, and in training sparse networks from scratch. Thus, our results provide the first support for sparse training on commodity hardware. acknowledgement: 'We would like to thank Elias Frantar for his valuable assistance and support at the outset of this project, and the anonymous ICML and SNN reviewers for very constructive feedback. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. DA acknowledges generous ERC support, via Starting Grant 805223 ScaleML. ' alternative_title: - PMLR article_processing_charge: No author: - first_name: Mahdi full_name: Nikdan, Mahdi id: 66374281-f394-11eb-9cf6-869147deecc0 last_name: Nikdan - first_name: Tommaso full_name: Pegolotti, Tommaso last_name: Pegolotti - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:26215-26227.' apa: 'Nikdan, M., Pegolotti, T., Iofinova, E. B., Kurtic, E., & Alistarh, D.-A. (2023). SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 26215–26227). Honolulu, Hawaii, HI, United States: ML Research Press.' chicago: 'Nikdan, Mahdi, Tommaso Pegolotti, Eugenia B Iofinova, Eldar Kurtic, and Dan-Adrian Alistarh. “SparseProp: Efficient Sparse Backpropagation for Faster Training of Neural Networks at the Edge.” In Proceedings of the 40th International Conference on Machine Learning, 202:26215–27. ML Research Press, 2023.' ieee: 'M. Nikdan, T. Pegolotti, E. B. Iofinova, E. Kurtic, and D.-A. Alistarh, “SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 26215–26227.' ista: 'Nikdan M, Pegolotti T, Iofinova EB, Kurtic E, Alistarh D-A. 2023. SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 26215–26227.' mla: 'Nikdan, Mahdi, et al. “SparseProp: Efficient Sparse Backpropagation for Faster Training of Neural Networks at the Edge.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 26215–27.' short: M. Nikdan, T. Pegolotti, E.B. Iofinova, E. Kurtic, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 26215–26227. conference: end_date: 2023-07-29 location: Honolulu, Hawaii, HI, United States name: 'ICML: International Conference on Machine Learning' start_date: 2023-07-23 date_created: 2023-10-29T23:01:17Z date_published: 2023-07-30T00:00:00Z date_updated: 2023-10-31T09:33:51Z day: '30' department: - _id: DaAl ec_funded: 1 external_id: arxiv: - '2302.04852' intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2302.04852 month: '07' oa: 1 oa_version: Preprint page: 26215-26227 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 40th International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: 'SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '14457' abstract: - lang: eng text: "Threshold secret sharing allows a dealer to split a secret s into n shares, such that any t shares allow for reconstructing s, but no t-1 shares reveal any information about s. Leakage-resilient secret sharing requires that the secret remains hidden, even when an adversary additionally obtains a limited amount of leakage from every share. Benhamouda et al. (CRYPTO’18) proved that Shamir’s secret sharing scheme is one bit leakage-resilient for reconstruction threshold t≥0.85n and conjectured that the same holds for t = c.n for any constant 0≤c≤1. Nielsen and Simkin (EUROCRYPT’20) showed that this is the best one can hope for by proving that Shamir’s scheme is not secure against one-bit leakage when t0c.n/log(n).\r\nIn this work, we strengthen the lower bound of Nielsen and Simkin. We consider noisy leakage-resilience, where a random subset of leakages is replaced by uniformly random noise. We prove a lower bound for Shamir’s secret sharing, similar to that of Nielsen and Simkin, which holds even when a constant fraction of leakages is replaced by random noise. To this end, we first prove a lower bound on the share size of any noisy-leakage-resilient sharing scheme. We then use this lower bound to show that there exist universal constants c1, c2, such that for sufficiently large n it holds that Shamir’s secret sharing scheme is not noisy-leakage-resilient for t≤c1.n/log(n), even when a c2 fraction of leakages are replaced by random noise.\r\n\r\n\r\n\r\n" alternative_title: - LNCS article_processing_charge: No author: - first_name: Charlotte full_name: Hoffmann, Charlotte id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7 last_name: Hoffmann orcid: 0000-0003-2027-5549 - first_name: Mark full_name: Simkin, Mark last_name: Simkin citation: ama: 'Hoffmann C, Simkin M. Stronger lower bounds for leakage-resilient secret sharing. In: 8th International Conference on Cryptology and Information Security in Latin America. Vol 14168. Springer Nature; 2023:215-228. doi:10.1007/978-3-031-44469-2_11' apa: 'Hoffmann, C., & Simkin, M. (2023). Stronger lower bounds for leakage-resilient secret sharing. In 8th International Conference on Cryptology and Information Security in Latin America (Vol. 14168, pp. 215–228). Quito, Ecuador: Springer Nature. https://doi.org/10.1007/978-3-031-44469-2_11' chicago: Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient Secret Sharing.” In 8th International Conference on Cryptology and Information Security in Latin America, 14168:215–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44469-2_11. ieee: C. Hoffmann and M. Simkin, “Stronger lower bounds for leakage-resilient secret sharing,” in 8th International Conference on Cryptology and Information Security in Latin America, Quito, Ecuador, 2023, vol. 14168, pp. 215–228. ista: 'Hoffmann C, Simkin M. 2023. Stronger lower bounds for leakage-resilient secret sharing. 8th International Conference on Cryptology and Information Security in Latin America. LATINCRYPT: Conference on Cryptology and Information Security in Latin America, LNCS, vol. 14168, 215–228.' mla: Hoffmann, Charlotte, and Mark Simkin. “Stronger Lower Bounds for Leakage-Resilient Secret Sharing.” 8th International Conference on Cryptology and Information Security in Latin America, vol. 14168, Springer Nature, 2023, pp. 215–28, doi:10.1007/978-3-031-44469-2_11. short: C. Hoffmann, M. Simkin, in:, 8th International Conference on Cryptology and Information Security in Latin America, Springer Nature, 2023, pp. 215–228. conference: end_date: 2023-10-06 location: Quito, Ecuador name: 'LATINCRYPT: Conference on Cryptology and Information Security in Latin America' start_date: 2023-10-03 date_created: 2023-10-29T23:01:16Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-10-31T11:43:12Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-031-44469-2_11 intvolume: ' 14168' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/1017 month: '10' oa: 1 oa_version: Preprint page: 215-228 publication: 8th International Conference on Cryptology and Information Security in Latin America publication_identifier: eissn: - 1611-3349 isbn: - '9783031444685' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Stronger lower bounds for leakage-resilient secret sharing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14168 year: '2023' ... --- _id: '14458' abstract: - lang: eng text: 'We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.' acknowledged_ssus: - _id: ScienComp acknowledgement: The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement No. 805223 ScaleML), as well as experimental support from Eldar Kurtic, and from the IST Austria IT department, in particular Stefano Elefante, Andrei Hornoiu, and Alois Schloegl. alternative_title: - PMLR article_processing_charge: No author: - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Frantar E, Alistarh D-A. SparseGPT: Massive language models can be accurately pruned in one-shot. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:10323-10337.' apa: 'Frantar, E., & Alistarh, D.-A. (2023). SparseGPT: Massive language models can be accurately pruned in one-shot. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 10323–10337). Honolulu, Hawaii, HI, United States: ML Research Press.' chicago: 'Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models Can Be Accurately Pruned in One-Shot.” In Proceedings of the 40th International Conference on Machine Learning, 202:10323–37. ML Research Press, 2023.' ieee: 'E. Frantar and D.-A. Alistarh, “SparseGPT: Massive language models can be accurately pruned in one-shot,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 10323–10337.' ista: 'Frantar E, Alistarh D-A. 2023. SparseGPT: Massive language models can be accurately pruned in one-shot. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 10323–10337.' mla: 'Frantar, Elias, and Dan-Adrian Alistarh. “SparseGPT: Massive Language Models Can Be Accurately Pruned in One-Shot.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 10323–37.' short: E. Frantar, D.-A. Alistarh, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 10323–10337. conference: end_date: 2023-07-29 location: Honolulu, Hawaii, HI, United States name: 'ICML: International Conference on Machine Learning' start_date: 2023-07-23 date_created: 2023-10-29T23:01:16Z date_published: 2023-07-30T00:00:00Z date_updated: 2023-10-31T09:59:42Z day: '30' department: - _id: DaAl ec_funded: 1 external_id: arxiv: - '2301.00774' intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.00774 month: '07' oa: 1 oa_version: Preprint page: 10323-10337 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 40th International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: 'SparseGPT: Massive language models can be accurately pruned in one-shot' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '14451' abstract: - lang: eng text: 'We investigate the potential of Multi-Objective, Deep Reinforcement Learning for stock and cryptocurrency single-asset trading: in particular, we consider a Multi-Objective algorithm which generalizes the reward functions and discount factor (i.e., these components are not specified a priori, but incorporated in the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT, XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of the proposed Multi-Objective algorithm, and provide preliminary statistical evidence showing increased predictive stability over the corresponding Single-Objective strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge over the corresponding Single-Objective strategy when the reward mechanism is sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss the generalization properties with respect to the discount factor. The entirety of our code is provided in open-source format.' acknowledgement: Open access funding provided by Università degli Studi di Trieste within the CRUI-CARE Agreement. Funding was provided by Austrian Science Fund (Grant No. F65), Horizon 2020 (Grant No. 754411) and Österreichische Forschungsförderungsgesellschaft. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Federico full_name: Cornalba, Federico id: 2CEB641C-A400-11E9-A717-D712E6697425 last_name: Cornalba orcid: 0000-0002-6269-5149 - first_name: Constantin full_name: Disselkamp, Constantin last_name: Disselkamp - first_name: Davide full_name: Scassola, Davide last_name: Scassola - first_name: Christopher full_name: Helf, Christopher last_name: Helf citation: ama: 'Cornalba F, Disselkamp C, Scassola D, Helf C. Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications. 2023. doi:10.1007/s00521-023-09033-7' apa: 'Cornalba, F., Disselkamp, C., Scassola, D., & Helf, C. (2023). Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications. Springer Nature. https://doi.org/10.1007/s00521-023-09033-7' chicago: 'Cornalba, Federico, Constantin Disselkamp, Davide Scassola, and Christopher Helf. “Multi-Objective Reward Generalization: Improving Performance of Deep Reinforcement Learning for Applications in Single-Asset Trading.” Neural Computing and Applications. Springer Nature, 2023. https://doi.org/10.1007/s00521-023-09033-7.' ieee: 'F. Cornalba, C. Disselkamp, D. Scassola, and C. Helf, “Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading,” Neural Computing and Applications. Springer Nature, 2023.' ista: 'Cornalba F, Disselkamp C, Scassola D, Helf C. 2023. Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading. Neural Computing and Applications.' mla: 'Cornalba, Federico, et al. “Multi-Objective Reward Generalization: Improving Performance of Deep Reinforcement Learning for Applications in Single-Asset Trading.” Neural Computing and Applications, Springer Nature, 2023, doi:10.1007/s00521-023-09033-7.' short: F. Cornalba, C. Disselkamp, D. Scassola, C. Helf, Neural Computing and Applications (2023). date_created: 2023-10-22T22:01:16Z date_published: 2023-10-05T00:00:00Z date_updated: 2023-10-31T10:58:28Z day: '05' department: - _id: JuFi doi: 10.1007/s00521-023-09033-7 ec_funded: 1 external_id: arxiv: - '2203.04579' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00521-023-09033-7 month: '10' oa: 1 oa_version: Published Version project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Neural Computing and Applications publication_identifier: eissn: - 1433-3058 issn: - 0941-0643 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14444' abstract: - lang: eng text: "We prove several results about substructures in Latin squares. First, we explain how to adapt our recent work on high-girth Steiner triple systems to the setting of Latin squares, resolving a conjecture of Linial that there exist Latin squares with arbitrarily high girth. As a consequence, we see that the number of order- n Latin squares with no intercalate (i.e., no 2×2 Latin subsquare) is at least (e−9/4n−o(n))n2. Equivalently, P[N=0]≥e−n2/4−o(n2)=e−(1+o(1))EN\r\n , where N is the number of intercalates in a uniformly random order- n Latin square. \r\nIn fact, extending recent work of Kwan, Sah, and Sawhney, we resolve the general large-deviation problem for intercalates in random Latin squares, up to constant factors in the exponent: for any constant 0<δ≤1 we have P[N≤(1−δ)EN]=exp(−Θ(n2)) and for any constant δ>0 we have P[N≥(1+δ)EN]=exp(−Θ(n4/3logn)). \r\nFinally, as an application of some new general tools for studying substructures in random Latin squares, we show that in almost all order- n Latin squares, the number of cuboctahedra (i.e., the number of pairs of possibly degenerate 2×2 submatrices with the same arrangement of symbols) is of order n4, which is the minimum possible. As observed by Gowers and Long, this number can be interpreted as measuring ``how associative'' the quasigroup associated with the Latin square is." acknowledgement: Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302. Sah was supported by the PD Soros Fellowship. Simkin was supported by the Center of Mathematical Sciences and Applications at Harvard University. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Ashwin full_name: Sah, Ashwin last_name: Sah - first_name: Mehtaab full_name: Sawhney, Mehtaab last_name: Sawhney - first_name: Michael full_name: Simkin, Michael last_name: Simkin citation: ama: Kwan MA, Sah A, Sawhney M, Simkin M. Substructures in Latin squares. Israel Journal of Mathematics. 2023;256(2):363-416. doi:10.1007/s11856-023-2513-9 apa: Kwan, M. A., Sah, A., Sawhney, M., & Simkin, M. (2023). Substructures in Latin squares. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-023-2513-9 chicago: Kwan, Matthew Alan, Ashwin Sah, Mehtaab Sawhney, and Michael Simkin. “Substructures in Latin Squares.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-023-2513-9. ieee: M. A. Kwan, A. Sah, M. Sawhney, and M. Simkin, “Substructures in Latin squares,” Israel Journal of Mathematics, vol. 256, no. 2. Springer Nature, pp. 363–416, 2023. ista: Kwan MA, Sah A, Sawhney M, Simkin M. 2023. Substructures in Latin squares. Israel Journal of Mathematics. 256(2), 363–416. mla: Kwan, Matthew Alan, et al. “Substructures in Latin Squares.” Israel Journal of Mathematics, vol. 256, no. 2, Springer Nature, 2023, pp. 363–416, doi:10.1007/s11856-023-2513-9. short: M.A. Kwan, A. Sah, M. Sawhney, M. Simkin, Israel Journal of Mathematics 256 (2023) 363–416. date_created: 2023-10-22T22:01:14Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-10-31T11:27:30Z day: '01' department: - _id: MaKw doi: 10.1007/s11856-023-2513-9 external_id: arxiv: - '2202.05088' intvolume: ' 256' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2202.05088 month: '09' oa: 1 oa_version: Preprint page: 363-416 publication: Israel Journal of Mathematics publication_identifier: eissn: - 1565-8511 issn: - 0021-2172 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Substructures in Latin squares type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 256 year: '2023' ... --- _id: '14454' abstract: - lang: eng text: As AI and machine-learned software are used increasingly for making decisions that affect humans, it is imperative that they remain fair and unbiased in their decisions. To complement design-time bias mitigation measures, runtime verification techniques have been introduced recently to monitor the algorithmic fairness of deployed systems. Previous monitoring techniques assume full observability of the states of the (unknown) monitored system. Moreover, they can monitor only fairness properties that are specified as arithmetic expressions over the probabilities of different events. In this work, we extend fairness monitoring to systems modeled as partially observed Markov chains (POMC), and to specifications containing arithmetic expressions over the expected values of numerical functions on event sequences. The only assumptions we make are that the underlying POMC is aperiodic and starts in the stationary distribution, with a bound on its mixing time being known. These assumptions enable us to estimate a given property for the entire distribution of possible executions of the monitored POMC, by observing only a single execution. Our monitors observe a long run of the system and, after each new observation, output updated PAC-estimates of how fair or biased the system is. The monitors are computationally lightweight and, using a prototype implementation, we demonstrate their effectiveness on several real-world examples. acknowledgement: 'This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Konstantin full_name: Kueffner, Konstantin id: 8121a2d0-dc85-11ea-9058-af578f3b4515 last_name: Kueffner orcid: 0000-0001-8974-2542 - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 citation: ama: 'Henzinger TA, Kueffner K, Mallik K. Monitoring algorithmic fairness under partial observations. In: 23rd International Conference on Runtime Verification. Vol 14245. Springer Nature; 2023:291-311. doi:10.1007/978-3-031-44267-4_15' apa: 'Henzinger, T. A., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness under partial observations. In 23rd International Conference on Runtime Verification (Vol. 14245, pp. 291–311). Thessaloniki, Greece: Springer Nature. https://doi.org/10.1007/978-3-031-44267-4_15' chicago: Henzinger, Thomas A, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness under Partial Observations.” In 23rd International Conference on Runtime Verification, 14245:291–311. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_15. ieee: T. A. Henzinger, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness under partial observations,” in 23rd International Conference on Runtime Verification, Thessaloniki, Greece, 2023, vol. 14245, pp. 291–311. ista: 'Henzinger TA, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness under partial observations. 23rd International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 14245, 291–311.' mla: Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness under Partial Observations.” 23rd International Conference on Runtime Verification, vol. 14245, Springer Nature, 2023, pp. 291–311, doi:10.1007/978-3-031-44267-4_15. short: T.A. Henzinger, K. Kueffner, K. Mallik, in:, 23rd International Conference on Runtime Verification, Springer Nature, 2023, pp. 291–311. conference: end_date: 2023-10-06 location: Thessaloniki, Greece name: 'RV: Conference on Runtime Verification' start_date: 2023-10-03 date_created: 2023-10-29T23:01:15Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-10-31T11:48:20Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-031-44267-4_15 ec_funded: 1 external_id: arxiv: - '2308.00341' intvolume: ' 14245' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2308.00341 month: '10' oa: 1 oa_version: Preprint page: 291-311 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 23rd International Conference on Runtime Verification publication_identifier: eissn: - 1611-3349 isbn: - '9783031442667' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Monitoring algorithmic fairness under partial observations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14245 year: '2023' ... --- _id: '14446' abstract: - lang: eng text: Recent work has paid close attention to the first principle of Granger causality, according to which cause precedes effect. In this context, the question may arise whether the detected direction of causality also reverses after the time reversal of unidirectionally coupled data. Recently, it has been shown that for unidirectionally causally connected autoregressive (AR) processes X → Y, after time reversal of data, the opposite causal direction Y → X is indeed detected, although typically as part of the bidirectional X↔ Y link. As we argue here, the answer is different when the measured data are not from AR processes but from linked deterministic systems. When the goal is the usual forward data analysis, cross-mapping-like approaches correctly detect X → Y, while Granger causality-like approaches, which should not be used for deterministic time series, detect causal independence X → Y. The results of backward causal analysis depend on the predictability of the reversed data. Unlike AR processes, observables from deterministic dynamical systems, even complex nonlinear ones, can be predicted well forward, while backward predictions can be difficult (notably when the time reversal of a function leads to one-to-many relations). To address this problem, we propose an approach based on models that provide multiple candidate predictions for the target, combined with a loss function that consideres only the best candidate. The resulting good forward and backward predictability supports the view that unidirectionally causally linked deterministic dynamical systems X → Y can be expected to detect the same link both before and after time reversal. acknowledgement: The work was supported by the Scientific Grant Agency of the Ministry of Education of the Slovak Republic and the Slovak Academy of Sciences, projects APVV-21-0216, VEGA2-0096-21 and VEGA 2-0023-22. article_processing_charge: Yes article_type: original author: - first_name: Jozef full_name: Jakubík, Jozef last_name: Jakubík - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai - first_name: Martina full_name: Chvosteková, Martina last_name: Chvosteková - first_name: Anna full_name: Krakovská, Anna last_name: Krakovská citation: ama: Jakubík J, Phuong M, Chvosteková M, Krakovská A. Against the flow of time with multi-output models. Measurement Science Review. 2023;23(4):175-183. doi:10.2478/msr-2023-0023 apa: Jakubík, J., Phuong, M., Chvosteková, M., & Krakovská, A. (2023). Against the flow of time with multi-output models. Measurement Science Review. Sciendo. https://doi.org/10.2478/msr-2023-0023 chicago: Jakubík, Jozef, Mary Phuong, Martina Chvosteková, and Anna Krakovská. “Against the Flow of Time with Multi-Output Models.” Measurement Science Review. Sciendo, 2023. https://doi.org/10.2478/msr-2023-0023. ieee: J. Jakubík, M. Phuong, M. Chvosteková, and A. Krakovská, “Against the flow of time with multi-output models,” Measurement Science Review, vol. 23, no. 4. Sciendo, pp. 175–183, 2023. ista: Jakubík J, Phuong M, Chvosteková M, Krakovská A. 2023. Against the flow of time with multi-output models. Measurement Science Review. 23(4), 175–183. mla: Jakubík, Jozef, et al. “Against the Flow of Time with Multi-Output Models.” Measurement Science Review, vol. 23, no. 4, Sciendo, 2023, pp. 175–83, doi:10.2478/msr-2023-0023. short: J. Jakubík, M. Phuong, M. Chvosteková, A. Krakovská, Measurement Science Review 23 (2023) 175–183. date_created: 2023-10-22T22:01:15Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-10-31T12:12:47Z day: '01' ddc: - '510' department: - _id: ChLa doi: 10.2478/msr-2023-0023 file: - access_level: open_access checksum: b069cc10fa6a7c96b2bc9f728165f9e6 content_type: application/pdf creator: dernst date_created: 2023-10-31T12:07:23Z date_updated: 2023-10-31T12:07:23Z file_id: '14476' file_name: 2023_MeasurementScienceRev_Jakubik.pdf file_size: 2639783 relation: main_file success: 1 file_date_updated: 2023-10-31T12:07:23Z has_accepted_license: '1' intvolume: ' 23' issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 175-183 publication: Measurement Science Review publication_identifier: eissn: - 1335-8871 publication_status: published publisher: Sciendo quality_controlled: '1' scopus_import: '1' status: public title: Against the flow of time with multi-output models tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2023' ... --- _id: '14441' abstract: - lang: eng text: We study the Fröhlich polaron model in R3, and establish the subleading term in the strong coupling asymptotics of its ground state energy, corresponding to the quantum corrections to the classical energy determined by the Pekar approximation. acknowledgement: Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Brooks M, Seiringer R. The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. 2023;404:287-337. doi:10.1007/s00220-023-04841-3' apa: 'Brooks, M., & Seiringer, R. (2023). The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04841-3' chicago: 'Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part I - The Quantum Correction to the Classical Energy.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04841-3.' ieee: 'M. Brooks and R. Seiringer, “The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy,” Communications in Mathematical Physics, vol. 404. Springer Nature, pp. 287–337, 2023.' ista: 'Brooks M, Seiringer R. 2023. The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy. Communications in Mathematical Physics. 404, 287–337.' mla: 'Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part I - The Quantum Correction to the Classical Energy.” Communications in Mathematical Physics, vol. 404, Springer Nature, 2023, pp. 287–337, doi:10.1007/s00220-023-04841-3.' short: M. Brooks, R. Seiringer, Communications in Mathematical Physics 404 (2023) 287–337. date_created: 2023-10-22T22:01:13Z date_published: 2023-11-01T00:00:00Z date_updated: 2023-10-31T12:22:51Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00220-023-04841-3 ec_funded: 1 external_id: arxiv: - '2207.03156' file: - access_level: open_access checksum: 1ae49b39247cb6b40ff75997381581b8 content_type: application/pdf creator: dernst date_created: 2023-10-31T12:21:39Z date_updated: 2023-10-31T12:21:39Z file_id: '14477' file_name: 2023_CommMathPhysics_Brooks.pdf file_size: 832375 relation: main_file success: 1 file_date_updated: 2023-10-31T12:21:39Z has_accepted_license: '1' intvolume: ' 404' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 287-337 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 404 year: '2023' ... --- _id: '14448' abstract: - lang: eng text: We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in [16], [35]. As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subroutine based on in-face Frank-Wolfe directions, introduced in [4] in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html. article_processing_charge: No author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Vol 2023. IEEE; 2023:11980-11989. doi:10.1109/CVPR52729.2023.01153' apa: 'Kolmogorov, V. (2023). Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Vol. 2023, pp. 11980–11989). Vancouver, Canada: IEEE. https://doi.org/10.1109/CVPR52729.2023.01153' chicago: 'Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial in-Face Frank-Wolfe Directions.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2023:11980–89. IEEE, 2023. https://doi.org/10.1109/CVPR52729.2023.01153.' ieee: 'V. Kolmogorov, “Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Vancouver, Canada, 2023, vol. 2023, pp. 11980–11989.' ista: 'Kolmogorov V. 2023. Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2023, 11980–11989.' mla: 'Kolmogorov, Vladimir. “Solving Relaxations of MAP-MRF Problems: Combinatorial in-Face Frank-Wolfe Directions.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, vol. 2023, IEEE, 2023, pp. 11980–89, doi:10.1109/CVPR52729.2023.01153.' short: V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 11980–11989. conference: end_date: 2023-06-24 location: Vancouver, Canada name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2023-06-17 date_created: 2023-10-22T22:01:16Z date_published: 2023-08-22T00:00:00Z date_updated: 2023-10-31T12:01:24Z day: '22' department: - _id: VlKo doi: 10.1109/CVPR52729.2023.01153 external_id: arxiv: - '2010.09567' intvolume: ' 2023' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2010.09567' month: '08' oa: 1 oa_version: Preprint page: 11980-11989 publication: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition publication_identifier: isbn: - '9798350301298' issn: - 1063-6919 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '12672' abstract: - lang: eng text: Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation. acknowledgement: The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L. article_number: '112132' article_processing_charge: Yes article_type: original author: - first_name: David B. full_name: Lyons, David B. last_name: Lyons - first_name: Amy full_name: Briffa, Amy last_name: Briffa - first_name: Shengbo full_name: He, Shengbo last_name: He - first_name: Jaemyung full_name: Choi, Jaemyung last_name: Choi - first_name: Elizabeth full_name: Hollwey, Elizabeth id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd last_name: Hollwey - first_name: Jack full_name: Colicchio, Jack last_name: Colicchio - first_name: Ian full_name: Anderson, Ian last_name: Anderson - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Martin full_name: Howard, Martin last_name: Howard - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 2023;42(3). doi:10.1016/j.celrep.2023.112132 apa: Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132 chicago: Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132. ieee: D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” Cell Reports, vol. 42, no. 3. Elsevier, 2023. ista: Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132. mla: Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no. 3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132. short: D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023). date_created: 2023-02-23T09:17:44Z date_published: 2023-03-28T00:00:00Z date_updated: 2023-11-02T12:23:45Z day: '28' ddc: - '580' department: - _id: DaZi - _id: XiFe doi: 10.1016/j.celrep.2023.112132 ec_funded: 1 external_id: isi: - '000944921600001' file: - access_level: open_access checksum: 6cbc44fdb18bf18834c9e2a5b9c67123 content_type: application/pdf creator: kschuh date_created: 2023-05-11T10:41:42Z date_updated: 2023-05-11T10:41:42Z file_id: '12941' file_name: 2023_CellReports_Lyons.pdf file_size: 8401261 relation: main_file success: 1 file_date_updated: 2023-05-11T10:41:42Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 62935a00-2b32-11ec-9570-eff30fa39068 call_identifier: H2020 grant_number: '725746' name: Quantitative analysis of DNA methylation maintenance with chromatin publication: Cell Reports publication_identifier: eissn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '13178' abstract: - lang: eng text: We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar. acknowledgement: This research was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.). article_processing_charge: Yes article_type: original author: - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Krzysztof full_name: Mysliwy, Krzysztof id: 316457FC-F248-11E8-B48F-1D18A9856A87 last_name: Mysliwy - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Mitrouskas DJ, Mysliwy K, Seiringer R. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. 2023;11:1-52. doi:10.1017/fms.2023.45 apa: Mitrouskas, D. J., Mysliwy, K., & Seiringer, R. (2023). Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. Cambridge University Press. https://doi.org/10.1017/fms.2023.45 chicago: Mitrouskas, David Johannes, Krzysztof Mysliwy, and Robert Seiringer. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” Forum of Mathematics. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.45. ieee: D. J. Mitrouskas, K. Mysliwy, and R. Seiringer, “Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron,” Forum of Mathematics, vol. 11. Cambridge University Press, pp. 1–52, 2023. ista: Mitrouskas DJ, Mysliwy K, Seiringer R. 2023. Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron. Forum of Mathematics. 11, 1–52. mla: Mitrouskas, David Johannes, et al. “Optimal Parabolic Upper Bound for the Energy-Momentum Relation of a Strongly Coupled Polaron.” Forum of Mathematics, vol. 11, Cambridge University Press, 2023, pp. 1–52, doi:10.1017/fms.2023.45. short: D.J. Mitrouskas, K. Mysliwy, R. Seiringer, Forum of Mathematics 11 (2023) 1–52. date_created: 2023-07-02T22:00:43Z date_published: 2023-06-13T00:00:00Z date_updated: 2023-11-02T12:30:50Z day: '13' ddc: - '500' department: - _id: RoSe doi: 10.1017/fms.2023.45 ec_funded: 1 external_id: arxiv: - '2203.02454' isi: - '001005008800001' file: - access_level: open_access checksum: f672eb7dd015c472c9a04f1b9bf9df7d content_type: application/pdf creator: alisjak date_created: 2023-07-03T10:36:25Z date_updated: 2023-07-03T10:36:25Z file_id: '13186' file_name: 2023_ForumofMathematics.Sigma_Mitrouskas.pdf file_size: 943192 relation: main_file success: 1 file_date_updated: 2023-07-03T10:36:25Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1-52 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Forum of Mathematics publication_identifier: eissn: - 2050-5094 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2023' ... --- _id: '14484' abstract: - lang: eng text: Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling. acknowledgement: We are grateful to Zena Hadjivasiliou for comments on this article. A.K. is supported by grants from the European Research Council under the European Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe (101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051), and by a grant from the European Research Council under the EU Horizon 2020 research and innovation program (742138). article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: James full_name: Briscoe, James last_name: Briscoe citation: ama: Kicheva A, Briscoe J. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 2023;39:91-121. doi:10.1146/annurev-cellbio-020823-011522 apa: Kicheva, A., & Briscoe, J. (2023). Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-020823-011522 chicago: Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2023. https://doi.org/10.1146/annurev-cellbio-020823-011522. ieee: A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,” Annual Review of Cell and Developmental Biology, vol. 39. Annual Reviews, pp. 91–121, 2023. ista: Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 39, 91–121. mla: Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology, vol. 39, Annual Reviews, 2023, pp. 91–121, doi:10.1146/annurev-cellbio-020823-011522. short: A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39 (2023) 91–121. date_created: 2023-11-05T23:00:53Z date_published: 2023-10-16T00:00:00Z date_updated: 2023-11-06T09:56:24Z day: '16' ddc: - '570' department: - _id: AnKi doi: 10.1146/annurev-cellbio-020823-011522 ec_funded: 1 external_id: pmid: - '37418774' file: - access_level: open_access checksum: 461726014cf5907010afbd418d3c13ec content_type: application/pdf creator: dernst date_created: 2023-11-06T09:47:50Z date_updated: 2023-11-06T09:47:50Z file_id: '14491' file_name: 2023_AnnualReviews_Kicheva.pdf file_size: 434819 relation: main_file success: 1 file_date_updated: 2023-11-06T09:47:50Z has_accepted_license: '1' intvolume: ' 39' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 91-121 pmid: 1 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F07802 name: Morphogen control of growth and pattern in the spinal cord publication: Annual Review of Cell and Developmental Biology publication_identifier: eissn: - 1530-8995 issn: - 1081-0706 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Control of tissue development by morphogens tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 39 year: '2023' ... --- _id: '14488' abstract: - lang: eng text: 'Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handling both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with individual latent spaces for identity and illumination. The prior model is learned in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis, even when applied to unseen subjects under uncontrolled illumination. This work is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide extensive evaluation and ablative studies of our model and also provide an application, where any face can be relighted using textual input.' acknowledgement: Open Access funding enabled and organized by Projekt DEAL. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Pramod full_name: Rao, Pramod last_name: Rao - first_name: B. R. full_name: Mallikarjun, B. R. last_name: Mallikarjun - first_name: Gereon full_name: Fox, Gereon last_name: Fox - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Fangneng full_name: Zhan, Fangneng last_name: Zhan - first_name: Ayush full_name: Tewari, Ayush last_name: Tewari - first_name: Christian full_name: Theobalt, Christian last_name: Theobalt - first_name: Mohamed full_name: Elgharib, Mohamed last_name: Elgharib citation: ama: Rao P, Mallikarjun BR, Fox G, et al. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. 2023. doi:10.1007/s11263-023-01899-3 apa: Rao, P., Mallikarjun, B. R., Fox, G., Weyrich, T., Bickel, B., Pfister, H., … Elgharib, M. (2023). A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-023-01899-3 chicago: Rao, Pramod, B. R. Mallikarjun, Gereon Fox, Tim Weyrich, Bernd Bickel, Hanspeter Pfister, Wojciech Matusik, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International Journal of Computer Vision. Springer Nature, 2023. https://doi.org/10.1007/s11263-023-01899-3. ieee: P. Rao et al., “A deeper analysis of volumetric relightiable faces,” International Journal of Computer Vision. Springer Nature, 2023. ista: Rao P, Mallikarjun BR, Fox G, Weyrich T, Bickel B, Pfister H, Matusik W, Zhan F, Tewari A, Theobalt C, Elgharib M. 2023. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. mla: Rao, Pramod, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International Journal of Computer Vision, Springer Nature, 2023, doi:10.1007/s11263-023-01899-3. short: P. Rao, B.R. Mallikarjun, G. Fox, T. Weyrich, B. Bickel, H. Pfister, W. Matusik, F. Zhan, A. Tewari, C. Theobalt, M. Elgharib, International Journal of Computer Vision (2023). date_created: 2023-11-05T23:00:54Z date_published: 2023-10-31T00:00:00Z date_updated: 2023-11-06T08:52:30Z day: '31' department: - _id: BeBi doi: 10.1007/s11263-023-01899-3 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s11263-023-01899-3 month: '10' oa: 1 oa_version: Published Version publication: International Journal of Computer Vision publication_identifier: eissn: - 1573-1405 issn: - 0920-5691 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A deeper analysis of volumetric relightiable faces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14487' abstract: - lang: eng text: High Mountain Asia (HMA) is among the most vulnerable water towers globally and yet future projections of water availability in and from its high-mountain catchments remain uncertain, as their hydrologic response to ongoing environmental changes is complex. Mechanistic modeling approaches incorporating cryospheric, hydrological, and vegetation processes in high spatial, temporal, and physical detail have never been applied for high-elevation catchments of HMA. We use a land surface model at high spatial and temporal resolution (100 m and hourly) to simulate the coupled dynamics of energy, water, and vegetation for the 350 km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological year against a large set of observations to gain insight into the partitioning of the water balance at the subseasonal scale and across elevation bands. During the simulated hydrological year, we find that evapotranspiration is a key component of the total water balance, as it causes about the equivalent of 20% of all the available precipitation or 154% of the water production from glacier melt in the basin to return directly to the atmosphere. The depletion of the cryospheric water budget is dominated by snow melt, but at high elevations is primarily dictated by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%) at the catchment scale, accounting for the equivalent of 11% of snowfall, 17% of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should consider sublimation and other evaporative fluxes explicitly, as otherwise water balance estimates can be ill-quantified. acknowledgement: This project has received funding from the JSPS-SNSF (Japan Society for the Promotion of Science and Swiss National Science Foundation) Bilateral Programmes project (HOPE, High-ele-vation precipitation in High Mountain Asia; Grant 183633), and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (RAVEN, Rapid mass losses of debris-covered glaciers in High Mountain Asia; Grant 772751). We want to thank in particular T. Gurung, S. Joshi, J. Shea, W. Immerzeel, and others involved, as well as ICIMOD, for their efforts over the past years in observing the meteorology of the Langtang catchment, collecting and organizing the data and making them publicly available. We also thank the National Geographic Society (Grant NGS-61784R-19) and the Mount Everest Foundation (reference 19-24) for providing fieldwork funding for C. L. Fyffe. We thank T. Kramer for help with the WSL Hyperion cluster. We are grate-ful for comments by three anonymous reviewers and the Associate Editor, who greatly helped to improve the manuscript further. Open access funding provided by ETH-Bereich Forschungsanstalten. article_number: e2022WR033841 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Simone full_name: Fatichi, Simone last_name: Fatichi - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Michael full_name: Mccarthy, Michael id: 22a2674a-61ce-11ee-94b5-d18813baf16f last_name: Mccarthy - first_name: Catriona Louise full_name: Fyffe, Catriona Louise id: 001b0422-8d15-11ed-bc51-cab6c037a228 last_name: Fyffe - first_name: Stefan full_name: Fugger, Stefan last_name: Fugger - first_name: Shaoting full_name: Ren, Shaoting last_name: Ren - first_name: Marin full_name: Kneib, Marin last_name: Kneib - first_name: Achille full_name: Jouberton, Achille last_name: Jouberton - first_name: Jakob full_name: Steiner, Jakob last_name: Steiner - first_name: Koji full_name: Fujita, Koji last_name: Fujita - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: 'Buri P, Fatichi S, Shaw T, et al. Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. 2023;59(10). doi:10.1029/2022WR033841' apa: 'Buri, P., Fatichi, S., Shaw, T., Miles, E. S., McCarthy, M., Fyffe, C. L., … Pellicciotti, F. (2023). Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. Wiley. https://doi.org/10.1029/2022WR033841' chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan S. Miles, Michael McCarthy, Catriona Louise Fyffe, Stefan Fugger, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High-Elevation Catchment.” Water Resources Research. Wiley, 2023. https://doi.org/10.1029/2022WR033841.' ieee: 'P. Buri et al., “Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment,” Water Resources Research, vol. 59, no. 10. Wiley, 2023.' ista: 'Buri P, Fatichi S, Shaw T, Miles ES, McCarthy M, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment. Water Resources Research. 59(10), e2022WR033841.' mla: 'Buri, Pascal, et al. “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High-Elevation Catchment.” Water Resources Research, vol. 59, no. 10, e2022WR033841, Wiley, 2023, doi:10.1029/2022WR033841.' short: P. Buri, S. Fatichi, T. Shaw, E.S. Miles, M. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, Water Resources Research 59 (2023). date_created: 2023-11-05T23:00:53Z date_published: 2023-10-25T00:00:00Z date_updated: 2023-11-07T08:12:34Z day: '25' ddc: - '550' department: - _id: FrPe doi: 10.1029/2022WR033841 file: - access_level: open_access checksum: 7ba9c87228dc09029b16bc800a0ef1a1 content_type: application/pdf creator: dernst date_created: 2023-11-07T08:10:44Z date_updated: 2023-11-07T08:10:44Z file_id: '14495' file_name: 2023_WaterResourcesResearch_Buri.pdf file_size: 5554901 relation: main_file success: 1 file_date_updated: 2023-11-07T08:10:44Z has_accepted_license: '1' intvolume: ' 59' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Water Resources Research publication_identifier: eissn: - 1944-7973 issn: - 0043-1397 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '14494' relation: research_data status: public scopus_import: '1' status: public title: 'Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 59 year: '2023' ... --- _id: '14485' abstract: - lang: eng text: "Batching is a technique that stores multiple keys/values in each node of a data structure. In sequential search data structures, batching reduces latency by reducing the number of cache misses and shortening the chain of pointers to dereference. Applying batching to concurrent data structures is challenging, because it is difficult to maintain the search property and keep contention low in the presence of batching.\r\nIn this paper, we present a general methodology for leveraging batching in concurrent search data structures, called BatchBoost. BatchBoost builds a search data structure from distinct \"data\" and \"index\" layers. The data layer’s purpose is to store a batch of key/value pairs in each of its nodes. The index layer uses an unmodified concurrent search data structure to route operations to a position in the data layer that is \"close\" to where the corresponding key should exist. The requirements on the index and data layers are low: with minimal effort, we were able to compose three highly scalable concurrent search data structures based on three original data structures as the index layers with a batched version of the Lazy List as the data layer. The resulting BatchBoost data structures provide significant performance improvements over their original counterparts." alternative_title: - LIPIcs article_number: '35' article_processing_charge: Yes author: - first_name: Vitaly full_name: Aksenov, Vitaly last_name: Aksenov - first_name: Michael full_name: Anoprenko, Michael last_name: Anoprenko - first_name: Alexander full_name: Fedorov, Alexander id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6 last_name: Fedorov - first_name: Michael full_name: Spear, Michael last_name: Spear citation: ama: 'Aksenov V, Anoprenko M, Fedorov A, Spear M. Brief announcement: BatchBoost: Universal batching for concurrent data structures. In: 37th International Symposium on Distributed Computing. Vol 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.DISC.2023.35' apa: 'Aksenov, V., Anoprenko, M., Fedorov, A., & Spear, M. (2023). Brief announcement: BatchBoost: Universal batching for concurrent data structures. In 37th International Symposium on Distributed Computing (Vol. 281). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2023.35' chicago: 'Aksenov, Vitaly, Michael Anoprenko, Alexander Fedorov, and Michael Spear. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” In 37th International Symposium on Distributed Computing, Vol. 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.DISC.2023.35.' ieee: 'V. Aksenov, M. Anoprenko, A. Fedorov, and M. Spear, “Brief announcement: BatchBoost: Universal batching for concurrent data structures,” in 37th International Symposium on Distributed Computing, L’Aquila, Italy, 2023, vol. 281.' ista: 'Aksenov V, Anoprenko M, Fedorov A, Spear M. 2023. Brief announcement: BatchBoost: Universal batching for concurrent data structures. 37th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 281, 35.' mla: 'Aksenov, Vitaly, et al. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” 37th International Symposium on Distributed Computing, vol. 281, 35, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.DISC.2023.35.' short: V. Aksenov, M. Anoprenko, A. Fedorov, M. Spear, in:, 37th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. conference: end_date: 2023-10-13 location: L'Aquila, Italy name: 'DISC: Symposium on Distributed Computing' start_date: 2023-10-09 date_created: 2023-11-05T23:00:53Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-11-07T07:48:01Z day: '01' ddc: - '000' department: - _id: GradSch doi: 10.4230/LIPIcs.DISC.2023.35 file: - access_level: open_access checksum: d9f8d2915cccdf2df5905b7cd1b4a560 content_type: application/pdf creator: dernst date_created: 2023-11-06T11:45:21Z date_updated: 2023-11-06T11:45:21Z file_id: '14492' file_name: 2023_LIPIcs_Aksenov.pdf file_size: 646665 relation: main_file success: 1 file_date_updated: 2023-11-06T11:45:21Z has_accepted_license: '1' intvolume: ' 281' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: 37th International Symposium on Distributed Computing publication_identifier: isbn: - '9783959773010' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: 'Brief announcement: BatchBoost: Universal batching for concurrent data structures' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 281 year: '2023' ... --- _id: '14486' abstract: - lang: eng text: We present a minimal model of ferroelectric large polarons, which are suggested as one of the mechanisms responsible for the unique charge transport properties of hybrid perovskites. We demonstrate that short-ranged charge–rotor interactions lead to long-range ferroelectric ordering of rotors, which strongly affects the carrier mobility. In the nonperturbative regime, where our theory cannot be reduced to any of the earlier models, we reveal that the polaron is characterized by large coherence length and a roughly tenfold increase of the effective mass as compared to the bare mass. These results are in good agreement with other theoretical predictions for ferroelectric polarons. Our model establishes a general phenomenological framework for ferroelectric polarons providing the starting point for future studies of their role in the transport properties of hybrid organic-inorganic perovskites. acknowledgement: We thank Zh. Alpichshev, A. Volosniev, and A. V. Zampetaki for fruitful discussions and comments. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). article_number: '043016' article_processing_charge: Yes article_type: original author: - first_name: Georgios full_name: Koutentakis, Georgios id: d7b23d3a-9e21-11ec-b482-f76739596b95 last_name: Koutentakis - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Koutentakis G, Ghazaryan A, Lemeshko M. Rotor lattice model of ferroelectric large polarons. Physical Review Research. 2023;5(4). doi:10.1103/PhysRevResearch.5.043016 apa: Koutentakis, G., Ghazaryan, A., & Lemeshko, M. (2023). Rotor lattice model of ferroelectric large polarons. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043016 chicago: Koutentakis, Georgios, Areg Ghazaryan, and Mikhail Lemeshko. “Rotor Lattice Model of Ferroelectric Large Polarons.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043016. ieee: G. Koutentakis, A. Ghazaryan, and M. Lemeshko, “Rotor lattice model of ferroelectric large polarons,” Physical Review Research, vol. 5, no. 4. American Physical Society, 2023. ista: Koutentakis G, Ghazaryan A, Lemeshko M. 2023. Rotor lattice model of ferroelectric large polarons. Physical Review Research. 5(4), 043016. mla: Koutentakis, Georgios, et al. “Rotor Lattice Model of Ferroelectric Large Polarons.” Physical Review Research, vol. 5, no. 4, 043016, American Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043016. short: G. Koutentakis, A. Ghazaryan, M. Lemeshko, Physical Review Research 5 (2023). date_created: 2023-11-05T23:00:53Z date_published: 2023-10-05T00:00:00Z date_updated: 2023-11-07T07:53:39Z day: '05' ddc: - '530' department: - _id: MiLe doi: 10.1103/PhysRevResearch.5.043016 ec_funded: 1 external_id: arxiv: - '2301.09875' file: - access_level: open_access checksum: cb8de8fed6e09df1a18bd5a5aec5c55c content_type: application/pdf creator: dernst date_created: 2023-11-07T07:52:46Z date_updated: 2023-11-07T07:52:46Z file_id: '14493' file_name: 2023_PhysReviewResearch_Koutentakis.pdf file_size: 1127522 relation: main_file success: 1 file_date_updated: 2023-11-07T07:52:46Z has_accepted_license: '1' intvolume: ' 5' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Review Research publication_identifier: issn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Rotor lattice model of ferroelectric large polarons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2023' ... --- _id: '14313' abstract: - lang: eng text: To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling. acknowledgement: The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology. article_number: '102443' article_processing_charge: No article_type: review author: - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443' apa: 'Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443' chicago: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.' ieee: 'L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.' ista: 'Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.' mla: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023, doi:10.1016/j.pbi.2023.102443.' short: L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023). date_created: 2023-09-10T22:01:11Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-11-07T08:17:13Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.pbi.2023.102443 external_id: pmid: - '37666097' file: - access_level: open_access checksum: 1c476c3414d2dfb0c85db0cb6cfd8a28 content_type: application/pdf creator: amally date_created: 2023-11-02T17:03:20Z date_updated: 2023-11-02T17:03:20Z file_id: '14482' file_name: Fiedler CurrOpinOlantBiol 2023_revised.pdf file_size: 737872 relation: main_file success: 1 file_date_updated: 2023-11-02T17:03:20Z has_accepted_license: '1' intvolume: ' 75' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version pmid: 1 publication: Current Opinion in Plant Biology publication_identifier: issn: - 1369-5266 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Rapid auxin signaling: Unknowns old and new' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 75 year: '2023' ... --- _id: '14494' abstract: - lang: eng text: "We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023).\r\n\r\nBuri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841" article_processing_charge: No author: - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Simone full_name: Fatichi, Simone last_name: Fatichi - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw - first_name: 'Evan ' full_name: 'Miles, Evan ' last_name: Miles - first_name: Michael full_name: McCarthy, Michael id: 22a2674a-61ce-11ee-94b5-d18813baf16f last_name: McCarthy - first_name: Catriona Louise full_name: Fyffe, Catriona Louise id: 001b0422-8d15-11ed-bc51-cab6c037a228 last_name: Fyffe - first_name: Stefan full_name: Fugger, Stefan last_name: Fugger - first_name: Shaoting full_name: Ren, Shaoting last_name: Ren - first_name: Marin full_name: Kneib, Marin last_name: Kneib - first_name: Achille full_name: Jouberton, Achille last_name: Jouberton - first_name: Jakob full_name: Steiner, Jakob last_name: Steiner - first_name: Koji full_name: Fujita, Koji last_name: Fujita - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: 'Buri P, Fatichi S, Shaw T, et al. Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” 2023. doi:10.5281/ZENODO.8402426' apa: 'Buri, P., Fatichi, S., Shaw, T., Miles, E., McCarthy, M., Fyffe, C. L., … Pellicciotti, F. (2023). Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” Zenodo. https://doi.org/10.5281/ZENODO.8402426' chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan Miles, Michael McCarthy, Catriona Louise Fyffe, Stefan Fugger, et al. “Model Output Data to ‘Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8402426.' ieee: 'P. Buri et al., “Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.’” Zenodo, 2023.' ista: 'Buri P, Fatichi S, Shaw T, Miles E, McCarthy M, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment’, Zenodo, 10.5281/ZENODO.8402426.' mla: 'Buri, Pascal, et al. Model Output Data to “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.” Zenodo, 2023, doi:10.5281/ZENODO.8402426.' short: P. Buri, S. Fatichi, T. Shaw, E. Miles, M. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, (2023). date_created: 2023-11-07T08:01:39Z date_published: 2023-10-03T00:00:00Z date_updated: 2023-11-07T08:12:35Z day: '03' ddc: - '550' department: - _id: FrPe doi: 10.5281/ZENODO.8402426 has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://10.5281/ZENODO.8402426 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14487' relation: used_in_publication status: public status: public title: 'Model output data to "Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment"' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14499' abstract: - lang: eng text: "An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper, we study edge statistics in Ramsey graphs, in particular obtaining very precise control of the distribution of the number of edges in a random vertex subset of a C-Ramsey graph. This brings together two ongoing lines of research: the study of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability for low-degree polynomials of independent random variables.\r\n\r\nThe proof proceeds via an ‘additive structure’ dichotomy on the degree sequence and involves a wide range of different tools from Fourier analysis, random matrix theory, the theory of Boolean functions, probabilistic combinatorics and low-rank approximation. In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright theorem on small-ball probability for polynomials of Gaussians, which we believe is of independent interest. One of the consequences of our result is the resolution of an old conjecture of Erdős and McKay, for which Erdős reiterated in several of his open problem collections and for which he offered one of his notorious monetary prizes." acknowledgement: Kwan was supported for part of this work by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-2141064. Sah was supported by the PD Soros Fellowship. Sauermann was supported by NSF Award DMS-2100157, and for part of this work by a Sloan Research Fellowship. article_number: e21 article_processing_charge: Yes article_type: original author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Ashwin full_name: Sah, Ashwin last_name: Sah - first_name: Lisa full_name: Sauermann, Lisa last_name: Sauermann - first_name: Mehtaab full_name: Sawhney, Mehtaab last_name: Sawhney citation: ama: Kwan MA, Sah A, Sauermann L, Sawhney M. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 2023;11. doi:10.1017/fmp.2023.17 apa: Kwan, M. A., Sah, A., Sauermann, L., & Sawhney, M. (2023). Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. Cambridge University Press. https://doi.org/10.1017/fmp.2023.17 chicago: Kwan, Matthew Alan, Ashwin Sah, Lisa Sauermann, and Mehtaab Sawhney. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi. Cambridge University Press, 2023. https://doi.org/10.1017/fmp.2023.17. ieee: M. A. Kwan, A. Sah, L. Sauermann, and M. Sawhney, “Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture,” Forum of Mathematics, Pi, vol. 11. Cambridge University Press, 2023. ista: Kwan MA, Sah A, Sauermann L, Sawhney M. 2023. Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture. Forum of Mathematics, Pi. 11, e21. mla: Kwan, Matthew Alan, et al. “Anticoncentration in Ramsey Graphs and a Proof of the Erdős–McKay Conjecture.” Forum of Mathematics, Pi, vol. 11, e21, Cambridge University Press, 2023, doi:10.1017/fmp.2023.17. short: M.A. Kwan, A. Sah, L. Sauermann, M. Sawhney, Forum of Mathematics, Pi 11 (2023). date_created: 2023-11-07T09:02:48Z date_published: 2023-08-24T00:00:00Z date_updated: 2023-11-07T09:18:57Z day: '24' ddc: - '510' department: - _id: MaKw doi: 10.1017/fmp.2023.17 external_id: arxiv: - '2208.02874' file: - access_level: open_access checksum: 54b824098d59073cc87a308d458b0a3e content_type: application/pdf creator: dernst date_created: 2023-11-07T09:16:23Z date_updated: 2023-11-07T09:16:23Z file_id: '14500' file_name: 2023_ForumMathematics_Kwan.pdf file_size: 1218719 relation: main_file success: 1 file_date_updated: 2023-11-07T09:16:23Z has_accepted_license: '1' intvolume: ' 11' keyword: - Discrete Mathematics and Combinatorics - Geometry and Topology - Mathematical Physics - Statistics and Probability - Algebra and Number Theory - Analysis language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: bd95085b-d553-11ed-ba76-e55d3349be45 grant_number: '101076777' name: Randomness and structure in combinatorics publication: Forum of Mathematics, Pi publication_identifier: issn: - 2050-5086 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2023' ... --- _id: '14294' abstract: - lang: eng text: Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways. article_processing_charge: No author: - first_name: Natasha I full_name: Edman, Natasha I last_name: Edman - first_name: Rachel L full_name: Redler, Rachel L last_name: Redler - first_name: Ashish full_name: Phal, Ashish last_name: Phal - first_name: Thomas full_name: Schlichthaerle, Thomas last_name: Schlichthaerle - first_name: Sanjay R full_name: Srivatsan, Sanjay R last_name: Srivatsan - first_name: Ali full_name: Etemadi, Ali last_name: Etemadi - first_name: Seong full_name: An, Seong last_name: An - first_name: Andrew full_name: Favor, Andrew last_name: Favor - first_name: Devon full_name: Ehnes, Devon last_name: Ehnes - first_name: Zhe full_name: Li, Zhe last_name: Li - first_name: Florian M full_name: Praetorius, Florian M id: dfec9381-4341-11ee-8fd8-faa02bba7d62 last_name: Praetorius - first_name: Max full_name: Gordon, Max last_name: Gordon - first_name: Wei full_name: Yang, Wei last_name: Yang - first_name: Brian full_name: Coventry, Brian last_name: Coventry - first_name: Derrick R full_name: Hicks, Derrick R last_name: Hicks - first_name: Longxing full_name: Cao, Longxing last_name: Cao - first_name: Neville full_name: Bethel, Neville last_name: Bethel - first_name: Piper full_name: Heine, Piper last_name: Heine - first_name: Analisa N full_name: Murray, Analisa N last_name: Murray - first_name: Stacey full_name: Gerben, Stacey last_name: Gerben - first_name: Lauren full_name: Carter, Lauren last_name: Carter - first_name: Marcos full_name: Miranda, Marcos last_name: Miranda - first_name: Babak full_name: Negahdari, Babak last_name: Negahdari - first_name: Sangwon full_name: Lee, Sangwon last_name: Lee - first_name: Cole full_name: Trapnell, Cole last_name: Trapnell - first_name: Lance full_name: Stewart, Lance last_name: Stewart - first_name: Damian C full_name: Ekiert, Damian C last_name: Ekiert - first_name: Joseph full_name: Schlessinger, Joseph last_name: Schlessinger - first_name: Jay full_name: Shendure, Jay last_name: Shendure - first_name: Gira full_name: Bhabha, Gira last_name: Bhabha - first_name: Hannele full_name: Ruohola-Baker, Hannele last_name: Ruohola-Baker - first_name: David full_name: Baker, David last_name: Baker citation: ama: Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv. doi:10.1101/2023.03.14.532666 apa: Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R., Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv. https://doi.org/10.1101/2023.03.14.532666 chicago: Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, n.d. https://doi.org/10.1101/2023.03.14.532666. ieee: N. I. Edman et al., “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies,” bioRxiv. . ista: Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv, 10.1101/2023.03.14.532666. mla: Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, doi:10.1101/2023.03.14.532666. short: N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi, S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry, D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M. Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger, J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.). date_created: 2023-09-06T12:31:49Z date_published: 2023-03-15T00:00:00Z date_updated: 2023-11-07T12:21:58Z day: '15' doi: 10.1101/2023.03.14.532666 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.03.14.532666 month: '03' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: submitted status: public title: Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14513' abstract: - lang: eng text: Cold atomic gases have become a paradigmatic system for exploring fundamental physics, which at the same time allows for applications in quantum technologies. The accelerating developments in the field have led to a highly advanced set of engineering techniques that, for example, can tune interactions, shape the external geometry, select among a large set of atomic species with different properties, or control the number of atoms. In particular, it is possible to operate in lower dimensions and drive atomic systems into the strongly correlated regime. In this review, we discuss recent advances in few-body cold atom systems confined in low dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in one dimension and provide an introduction to the static properties before we review the state-of-the-art research into quantum dynamical processes stimulated by the presence of correlations. Besides discussing the fundamental physical phenomena arising in these systems, we also provide an overview of the calculational and numerical tools and methods that are commonly used, thus delivering a balanced and comprehensive overview of the field. We conclude by giving an outlook on possible future directions that are interesting to explore in these correlated systems. acknowledgement: This review could not have been written without the many fruitful discussions and great collaborations with colleagues throughout the years, there are too many to mention. Here we acknowledge conversations regarding the context of the review with Joachim Brand, Fabian Brauneis, Adolfo del Campo, Alberto Cappellaro, Panagiotis Giannakeas, Tommaso Macrí, Oleksandr Marchukov, Lukas Rammelmüller and Manuel Valiente. S. I. M. acknowledges support from the NSF through a grant for ITAMP at Harvard University. T.F. acknowledges support from JSPS KAKENHI Grant Number JP23K03290 and T.F. and Th.B. acknowledge support from the Okinawa Institute for Science and Technology Graduate University, and JST Grant Number JPMJPF2221. A.F. and R. E. B. acknowledge support from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) - Edital Universal 406563/2021-7. A. G. V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. P. S. is supported by the Cluster of Excellence ‘Advanced Imaging of Matter’ of the Deutsche Forschungsgemeinschaft (DFG) - EXC2056 - project ID 390715994. N. T. Z. is partially supported by the Independent Research Fund Denmark . article_processing_charge: No article_type: original author: - first_name: S. I. full_name: Mistakidis, S. I. last_name: Mistakidis - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: R. E. full_name: Barfknecht, R. E. last_name: Barfknecht - first_name: T. full_name: Fogarty, T. last_name: Fogarty - first_name: Th full_name: Busch, Th last_name: Busch - first_name: A. full_name: Foerster, A. last_name: Foerster - first_name: P. full_name: Schmelcher, P. last_name: Schmelcher - first_name: N. T. full_name: Zinner, N. T. last_name: Zinner citation: ama: Mistakidis SI, Volosniev A, Barfknecht RE, et al. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. 2023;1042:1-108. doi:10.1016/j.physrep.2023.10.004 apa: Mistakidis, S. I., Volosniev, A., Barfknecht, R. E., Fogarty, T., Busch, T., Foerster, A., … Zinner, N. T. (2023). Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. Elsevier. https://doi.org/10.1016/j.physrep.2023.10.004 chicago: Mistakidis, S. I., Artem Volosniev, R. E. Barfknecht, T. Fogarty, Th Busch, A. Foerster, P. Schmelcher, and N. T. Zinner. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” Physics Reports. Elsevier, 2023. https://doi.org/10.1016/j.physrep.2023.10.004. ieee: S. I. Mistakidis et al., “Few-body Bose gases in low dimensions - A laboratory for quantum dynamics,” Physics Reports, vol. 1042. Elsevier, pp. 1–108, 2023. ista: Mistakidis SI, Volosniev A, Barfknecht RE, Fogarty T, Busch T, Foerster A, Schmelcher P, Zinner NT. 2023. Few-body Bose gases in low dimensions - A laboratory for quantum dynamics. Physics Reports. 1042, 1–108. mla: Mistakidis, S. I., et al. “Few-Body Bose Gases in Low Dimensions - A Laboratory for Quantum Dynamics.” Physics Reports, vol. 1042, Elsevier, 2023, pp. 1–108, doi:10.1016/j.physrep.2023.10.004. short: S.I. Mistakidis, A. Volosniev, R.E. Barfknecht, T. Fogarty, T. Busch, A. Foerster, P. Schmelcher, N.T. Zinner, Physics Reports 1042 (2023) 1–108. date_created: 2023-11-12T23:00:54Z date_published: 2023-11-29T00:00:00Z date_updated: 2023-11-13T08:01:57Z day: '29' department: - _id: MiLe doi: 10.1016/j.physrep.2023.10.004 ec_funded: 1 external_id: arxiv: - '2202.11071' intvolume: ' 1042' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2202.11071 month: '11' oa: 1 oa_version: Preprint page: 1-108 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physics Reports publication_identifier: issn: - 0370-1573 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Few-body Bose gases in low dimensions - A laboratory for quantum dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1042 year: '2023' ... --- _id: '12869' abstract: - lang: eng text: 'We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. ' acknowledgement: 'FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ' article_processing_charge: No author: - first_name: Frederik Ravn full_name: Klausen, Frederik Ravn last_name: Klausen - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: 'Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869' apa: 'Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869' chicago: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.' ieee: 'F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.' ista: 'Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.' mla: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.' short: F.R. Klausen, A.B. Lauritsen, (2023). date_created: 2023-04-26T12:34:49Z date_published: 2023-04-26T00:00:00Z date_updated: 2023-11-13T07:47:29Z day: '26' ddc: - '000' department: - _id: GradSch - _id: RoSe doi: 10.15479/AT:ISTA:12869 file: - access_level: open_access checksum: 85ede12d38bb8d944022a8cba4d719f5 content_type: application/octet-stream creator: alaurits date_created: 2023-04-26T12:30:06Z date_updated: 2023-04-26T12:30:06Z file_id: '12870' file_name: README.md file_size: 4567 relation: main_file success: 1 - access_level: open_access checksum: 25bf79452ae895f9c8a20571a096b4c3 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:27:34Z date_updated: 2023-04-26T12:27:34Z file_id: '12871' file_name: simulations_era=10_flux_varied_europe.zip file_size: 732586731 relation: main_file success: 1 - access_level: open_access checksum: bca48d80ece73eb169aee7211a4a751a content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:29:53Z date_updated: 2023-04-26T12:29:53Z file_id: '12872' file_name: simulations_era=10_flux_varied_torus.zip file_size: 1743893150 relation: main_file success: 1 - access_level: open_access checksum: e77a655db15486a387a36362fbf0b665 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:29:19Z date_updated: 2023-04-26T12:29:19Z file_id: '12873' file_name: simulations_era=10_R_varied_torus.zip file_size: 878391851 relation: main_file success: 1 - access_level: open_access checksum: 8556406513adc4aa2e0417f46680f627 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:30:05Z date_updated: 2023-04-26T12:30:05Z file_id: '12874' file_name: simulations_era=100.zip file_size: 201652478 relation: main_file success: 1 file_date_updated: 2023-04-26T12:30:06Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14505' relation: used_in_publication status: for_moderation - id: '12890' relation: used_in_publication status: public status: public title: 'Research data for: A stochastic cellular automaton model of culture formation' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12890' abstract: - lang: eng text: We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders. acknowledgement: Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. article_number: '054307' article_processing_charge: No article_type: original author: - first_name: Frederik Ravn full_name: Klausen, Frederik Ravn last_name: Klausen - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307 apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.108.054307 chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307. ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” Physical Review E, vol. 108, no. 5. American Physical Society, 2023. ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307. mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307. short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023). date_created: 2023-05-04T08:35:01Z date_published: 2023-11-08T00:00:00Z date_updated: 2023-11-13T07:47:30Z day: '08' department: - _id: GradSch - _id: RoSe doi: 10.1103/PhysRevE.108.054307 external_id: arxiv: - '2305.02153' intvolume: ' 108' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2305.02153 month: '11' oa: 1 oa_version: Preprint publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/FrederikRavnKlausen/model-for-culture-formation record: - id: '12869' relation: research_data status: public scopus_import: '1' status: public title: Stochastic cellular automaton model of culture formation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '14516' abstract: - lang: eng text: 'We revisit decentralized random beacons with a focus on practical distributed applications. Decentralized random beacons (Beaver and So, Eurocrypt''93) provide the functionality for n parties to generate an unpredictable sequence of bits in a way that cannot be biased, which is useful for any decentralized protocol requiring trusted randomness. Existing beacon constructions are highly inefficient in practical settings where protocol parties need to rejoin after crashes or disconnections, and more significantly where smart contracts may rely on arbitrary index points in high-volume streams. For this, we introduce a new notion of history-generating decentralized random beacons (HGDRBs). Roughly, the history-generation property of HGDRBs allows for previous beacon outputs to be efficiently generated knowing only the current value and the public key. At application layers, history-generation supports registering a sparser set of on-chain values if desired, so that apps like lotteries can utilize on-chain values without incurring high-frequency costs, enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose chains. Unlike rollups, HG is tailored specifically to recovering and verifying pseudorandom bit sequences and thus enjoys unique optimizations investigated in this work. We introduce STROBE: an efficient HGDRB construction which generalizes the original squaring-based RSA approach of Beaver and So. STROBE enjoys several useful properties that make it suited for practical applications that use beacons: 1) history-generating: it can regenerate and verify high-throughput beacon streams, supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying: NIZK-free, with state and validation employing a single ring element; 3) eco-friendly: stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient: the last beacon suffices to derive all past outputs, thus O(1) storage requirements for nodes serving the whole history.' acknowledgement: Work done when all the authors were at Novi Research, Meta. alternative_title: - LIPIcs article_number: '7' article_processing_charge: Yes author: - first_name: Donald full_name: Beaver, Donald last_name: Beaver - first_name: Mahimna full_name: Kelkar, Mahimna last_name: Kelkar - first_name: Kevin full_name: Lewi, Kevin last_name: Lewi - first_name: Valeria full_name: Nikolaenko, Valeria last_name: Nikolaenko - first_name: Alberto full_name: Sonnino, Alberto last_name: Sonnino - first_name: Konstantinos full_name: Chalkias, Konstantinos last_name: Chalkias - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Ladi De full_name: Naurois, Ladi De last_name: Naurois - first_name: Arnab full_name: Roy, Arnab last_name: Roy citation: ama: 'Beaver D, Kelkar M, Lewi K, et al. STROBE: Streaming Threshold Random Beacons. In: 5th Conference on Advances in Financial Technologies. Vol 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.AFT.2023.7' apa: 'Beaver, D., Kelkar, M., Lewi, K., Nikolaenko, V., Sonnino, A., Chalkias, K., … Roy, A. (2023). STROBE: Streaming Threshold Random Beacons. In 5th Conference on Advances in Financial Technologies (Vol. 282). Princeton, NJ, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.AFT.2023.7' chicago: 'Beaver, Donald, Mahimna Kelkar, Kevin Lewi, Valeria Nikolaenko, Alberto Sonnino, Konstantinos Chalkias, Eleftherios Kokoris Kogias, Ladi De Naurois, and Arnab Roy. “STROBE: Streaming Threshold Random Beacons.” In 5th Conference on Advances in Financial Technologies, Vol. 282. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.AFT.2023.7.' ieee: 'D. Beaver et al., “STROBE: Streaming Threshold Random Beacons,” in 5th Conference on Advances in Financial Technologies, Princeton, NJ, United States, 2023, vol. 282.' ista: 'Beaver D, Kelkar M, Lewi K, Nikolaenko V, Sonnino A, Chalkias K, Kokoris Kogias E, Naurois LD, Roy A. 2023. STROBE: Streaming Threshold Random Beacons. 5th Conference on Advances in Financial Technologies. AFT: Conference on Advances in Financial Technologies, LIPIcs, vol. 282, 7.' mla: 'Beaver, Donald, et al. “STROBE: Streaming Threshold Random Beacons.” 5th Conference on Advances in Financial Technologies, vol. 282, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.AFT.2023.7.' short: D. Beaver, M. Kelkar, K. Lewi, V. Nikolaenko, A. Sonnino, K. Chalkias, E. Kokoris Kogias, L.D. Naurois, A. Roy, in:, 5th Conference on Advances in Financial Technologies, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. conference: end_date: 2023-10-25 location: Princeton, NJ, United States name: 'AFT: Conference on Advances in Financial Technologies' start_date: 2023-10-23 date_created: 2023-11-12T23:00:55Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-11-13T08:52:01Z day: '01' ddc: - '000' department: - _id: ElKo doi: 10.4230/LIPIcs.AFT.2023.7 file: - access_level: open_access checksum: c1f98831cb5149d6c030c41999e6e960 content_type: application/pdf creator: dernst date_created: 2023-11-13T08:44:34Z date_updated: 2023-11-13T08:44:34Z file_id: '14521' file_name: 2023_LIPIcs_Beaver.pdf file_size: 793495 relation: main_file success: 1 file_date_updated: 2023-11-13T08:44:34Z has_accepted_license: '1' intvolume: ' 282' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/1643 month: '10' oa: 1 oa_version: Published Version publication: 5th Conference on Advances in Financial Technologies publication_identifier: isbn: - '9783959773034' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: 'STROBE: Streaming Threshold Random Beacons' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 282 year: '2023' ... --- _id: '14517' abstract: - lang: eng text: 'State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. ' acknowledged_ssus: - _id: NanoFab acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105), the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences, and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility." article_number: '044054' article_processing_charge: No article_type: original author: - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: 'Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 2023;20(4). doi:10.1103/PhysRevApplied.20.044054' apa: 'Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.20.044054' chicago: 'Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.20.044054.' ieee: 'M. Zemlicka et al., “Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses,” Physical Review Applied, vol. 20, no. 4. American Physical Society, 2023.' ista: 'Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 20(4), 044054.' mla: 'Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied, vol. 20, no. 4, 044054, American Physical Society, 2023, doi:10.1103/PhysRevApplied.20.044054.' short: M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, Physical Review Applied 20 (2023). date_created: 2023-11-12T23:00:55Z date_published: 2023-10-20T00:00:00Z date_updated: 2023-11-13T09:22:47Z day: '20' department: - _id: JoFi doi: 10.1103/PhysRevApplied.20.044054 ec_funded: 1 external_id: arxiv: - '2206.14104' intvolume: ' 20' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2206.14104 month: '10' oa: 1 oa_version: Preprint project: - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM' - _id: bdb7cfc1-d553-11ed-ba76-d2eaab167738 grant_number: '101080139' name: Open Superconducting Quantum Computers (OpenSuperQPlus) publication: Physical Review Applied publication_identifier: eissn: - 2331-7019 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '14520' relation: research_data status: public scopus_import: '1' status: public title: 'Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2023' ... --- _id: '14515' abstract: - lang: eng text: Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger. acknowledgement: "We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis, and Daan Frenkel for useful discussions and a careful reading of the manuscript, and we thank Age Tjalma for support with obtaining the Gaussian approximation of the chemotaxis system. This work is part of the Dutch Research Council (NWO) and was performed at the research institute AMOLF. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant (024.003.019)." article_number: '041017' article_processing_charge: Yes article_type: original author: - first_name: Manuel full_name: Reinhardt, Manuel last_name: Reinhardt - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Pieter Rein full_name: Ten Wolde, Pieter Rein last_name: Ten Wolde citation: ama: 'Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017' apa: 'Reinhardt, M., Tkačik, G., & Ten Wolde, P. R. (2023). Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.041017' chicago: 'Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017.' ieee: 'M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” Physical Review X, vol. 13, no. 4. American Physical Society, 2023.' ista: 'Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 13(4), 041017.' mla: 'Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.' short: M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023). date_created: 2023-11-12T23:00:55Z date_published: 2023-10-26T00:00:00Z date_updated: 2023-11-13T09:03:30Z day: '26' ddc: - '530' department: - _id: GaTk doi: 10.1103/PhysRevX.13.041017 external_id: arxiv: - '2203.03461' file: - access_level: open_access checksum: 32574aeebcca7347a4152c611b66b3d5 content_type: application/pdf creator: dernst date_created: 2023-11-13T09:00:19Z date_updated: 2023-11-13T09:00:19Z file_id: '14522' file_name: 2023_PhysReviewX_Reinhardt.pdf file_size: 1595223 relation: main_file success: 1 file_date_updated: 2023-11-13T09:00:19Z has_accepted_license: '1' intvolume: ' 13' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Physical Review X publication_identifier: eissn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2023' ... --- _id: '14514' abstract: - lang: eng text: 'The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines.' acknowledgement: "We are grateful to Dominic Vella, Jens Eggers, John Kolinski, Joshua Dijksman, and Daniel Bonn for insightful discussions. J. B. and A. S. acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC) through New Investigator Award No. EP/\r\nT000961/1. A. S. acknowledges the support of Royal Society under Grant No. RGS/R2/202135. J. E. S. acknowledges EPSRC Grants No. EP/N016602/1, EP/S022848/1, EP/S029966/1, and EP/P031684/1." article_number: '168201' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jack full_name: Binysh, Jack last_name: Binysh - first_name: Indrajit full_name: Chakraborty, Indrajit last_name: Chakraborty - first_name: Mykyta V. full_name: Chubynsky, Mykyta V. last_name: Chubynsky - first_name: Vicente L full_name: Diaz Melian, Vicente L id: b6798902-eea0-11ea-9cbc-a8e14286c631 last_name: Diaz Melian - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: James E. full_name: Sprittles, James E. last_name: Sprittles - first_name: Anton full_name: Souslov, Anton last_name: Souslov citation: ama: Binysh J, Chakraborty I, Chubynsky MV, et al. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 2023;131(16). doi:10.1103/PhysRevLett.131.168201 apa: Binysh, J., Chakraborty, I., Chubynsky, M. V., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J. E., & Souslov, A. (2023). Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.168201 chicago: Binysh, Jack, Indrajit Chakraborty, Mykyta V. Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James E. Sprittles, and Anton Souslov. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.168201. ieee: J. Binysh et al., “Modeling Leidenfrost levitation of soft elastic solids,” Physical Review Letters, vol. 131, no. 16. American Physical Society, 2023. ista: Binysh J, Chakraborty I, Chubynsky MV, Diaz Melian VL, Waitukaitis SR, Sprittles JE, Souslov A. 2023. Modeling Leidenfrost levitation of soft elastic solids. Physical Review Letters. 131(16), 168201. mla: Binysh, Jack, et al. “Modeling Leidenfrost Levitation of Soft Elastic Solids.” Physical Review Letters, vol. 131, no. 16, 168201, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.168201. short: J. Binysh, I. Chakraborty, M.V. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J.E. Sprittles, A. Souslov, Physical Review Letters 131 (2023). date_created: 2023-11-12T23:00:55Z date_published: 2023-10-20T00:00:00Z date_updated: 2023-11-13T09:21:30Z day: '20' ddc: - '530' department: - _id: ScWa doi: 10.1103/PhysRevLett.131.168201 file: - access_level: open_access checksum: 1a419e25b762aadffbcc8eb2e609bd97 content_type: application/pdf creator: dernst date_created: 2023-11-13T09:12:58Z date_updated: 2023-11-13T09:12:58Z file_id: '14524' file_name: 2023_PhysRevLetters_Binysh.pdf file_size: 724098 relation: main_file success: 1 file_date_updated: 2023-11-13T09:12:58Z has_accepted_license: '1' intvolume: ' 131' issue: '16' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '14523' relation: research_data status: public scopus_import: '1' status: public title: Modeling Leidenfrost levitation of soft elastic solids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2023' ... --- _id: '14523' abstract: - lang: eng text: see Readme file article_processing_charge: No author: - first_name: Jack full_name: Binysh, Jack last_name: Binysh - first_name: Indrajit full_name: Chakraborty, Indrajit last_name: Chakraborty - first_name: Mykyta full_name: Chubynsky, Mykyta last_name: Chubynsky - first_name: Vicente L full_name: Diaz Melian, Vicente L id: b6798902-eea0-11ea-9cbc-a8e14286c631 last_name: Diaz Melian - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: James full_name: Sprittles, James last_name: Sprittles - first_name: Anton full_name: Souslov, Anton last_name: Souslov citation: ama: 'Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. 2023. doi:10.5281/ZENODO.8329143' apa: 'Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J., & Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. Zenodo. https://doi.org/10.5281/ZENODO.8329143' chicago: 'Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8329143.' ieee: 'J. Binysh et al., “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1.” Zenodo, 2023.' ista: 'Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1, Zenodo, 10.5281/ZENODO.8329143.' mla: 'Binysh, Jack, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1. Zenodo, 2023, doi:10.5281/ZENODO.8329143.' short: J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023). date_created: 2023-11-13T09:12:11Z date_published: 2023-09-08T00:00:00Z date_updated: 2023-11-13T09:21:31Z day: '08' ddc: - '530' department: - _id: ScWa doi: 10.5281/ZENODO.8329143 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.8329143 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14514' relation: used_in_publication status: public status: public title: 'SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14518' abstract: - lang: eng text: We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets. acknowledgement: This research was supported in part by ISF grant no. 1679/21, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie Grant Agreement No. 665385. article_processing_charge: No author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 - first_name: Suman full_name: Sadhukhan, Suman last_name: Sadhukhan - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 citation: ama: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman discrete-bidding games. In: Frontiers in Artificial Intelligence and Applications. Vol 372. IOS Press; 2023:141-148. doi:10.3233/FAIA230264' apa: 'Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., & Zikelic, D. (2023). Reachability poorman discrete-bidding games. In Frontiers in Artificial Intelligence and Applications (Vol. 372, pp. 141–148). Krakow, Poland: IOS Press. https://doi.org/10.3233/FAIA230264' chicago: Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde Zikelic. “Reachability Poorman Discrete-Bidding Games.” In Frontiers in Artificial Intelligence and Applications, 372:141–48. IOS Press, 2023. https://doi.org/10.3233/FAIA230264. ieee: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability poorman discrete-bidding games,” in Frontiers in Artificial Intelligence and Applications, Krakow, Poland, 2023, vol. 372, pp. 141–148. ista: 'Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications. ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.' mla: Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” Frontiers in Artificial Intelligence and Applications, vol. 372, IOS Press, 2023, pp. 141–48, doi:10.3233/FAIA230264. short: G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148. conference: end_date: 2023-10-04 location: Krakow, Poland name: 'ECAI: European Conference on Artificial Intelligence' start_date: 2023-09-30 date_created: 2023-11-12T23:00:56Z date_published: 2023-09-28T00:00:00Z date_updated: 2023-11-13T10:18:45Z day: '28' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.3233/FAIA230264 ec_funded: 1 external_id: arxiv: - '2307.15218' file: - access_level: open_access checksum: 1390ca38480fa4cf286b0f1a42e8c12f content_type: application/pdf creator: dernst date_created: 2023-11-13T10:16:10Z date_updated: 2023-11-13T10:16:10Z file_id: '14529' file_name: 2023_FAIA_Avni.pdf file_size: 501011 relation: main_file success: 1 file_date_updated: 2023-11-13T10:16:10Z has_accepted_license: '1' intvolume: ' 372' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '09' oa: 1 oa_version: Published Version page: 141-148 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: Frontiers in Artificial Intelligence and Applications publication_identifier: isbn: - '9781643684369' issn: - 0922-6389 publication_status: published publisher: IOS Press quality_controlled: '1' scopus_import: '1' status: public title: Reachability poorman discrete-bidding games tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 372 year: '2023' ... --- _id: '13096' abstract: - lang: eng text: Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death. acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: "This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Morris full_name: Degen, Morris last_name: Degen - first_name: José Carlos full_name: Santos, José Carlos last_name: Santos - first_name: Kristyna full_name: Pluhackova, Kristyna last_name: Pluhackova - first_name: Gonzalo full_name: Cebrero, Gonzalo last_name: Cebrero - first_name: Saray full_name: Ramos, Saray last_name: Ramos - first_name: Gytis full_name: Jankevicius, Gytis last_name: Jankevicius - first_name: Ella full_name: Hartenian, Ella last_name: Hartenian - first_name: Undina full_name: Guillerm, Undina id: bb74f472-ae54-11eb-9835-bc9c22fb1183 last_name: Guillerm - first_name: Stefania A. full_name: Mari, Stefania A. last_name: Mari - first_name: Bastian full_name: Kohl, Bastian last_name: Kohl - first_name: Daniel J. full_name: Müller, Daniel J. last_name: Müller - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Timm full_name: Maier, Timm last_name: Maier - first_name: Camilo full_name: Perez, Camilo last_name: Perez - first_name: Christian full_name: Sieben, Christian last_name: Sieben - first_name: Petr full_name: Broz, Petr last_name: Broz - first_name: Sebastian full_name: Hiller, Sebastian last_name: Hiller citation: ama: Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 2023;618:1065-1071. doi:10.1038/s41586-023-05991-z apa: Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-05991-z chicago: Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-05991-z. ieee: M. Degen et al., “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” Nature, vol. 618. Springer Nature, pp. 1065–1071, 2023. ista: Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071. mla: Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:10.1038/s41586-023-05991-z. short: M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071. date_created: 2023-05-28T22:01:04Z date_published: 2023-06-29T00:00:00Z date_updated: 2023-11-14T11:49:21Z day: '29' ddc: - '570' department: - _id: PaSc doi: 10.1038/s41586-023-05991-z external_id: isi: - '000991386800011' file: - access_level: open_access checksum: 0fab69252453bff1de7f0e2eceb76d34 content_type: application/pdf creator: dernst date_created: 2023-11-14T11:48:18Z date_updated: 2023-11-14T11:48:18Z file_id: '14533' file_name: 2023_Nature_Degen.pdf file_size: 12292188 relation: main_file success: 1 file_date_updated: 2023-11-14T11:48:18Z has_accepted_license: '1' intvolume: ' 618' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1065-1071 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 618 year: '2023' ... --- _id: '13041' abstract: - lang: eng text: A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance. acknowledgement: The authors (N.L.F and R.B.J) would like to acknowledge the funding contributions of Shell and the EPRSC via I–Case studentships (grants no. EP/V519662/1 and EP/R511870/1 respectively). T.I would like to thank the ERC advanced Investigator Grant for CPG (EC H2020 835073). Thank you to Zhen Wang from the University of Cambridge for measuring GPC, the Yusuf Hamied Department of Chemistry's mass spectrometry service for MS measurements and analysis and Dr Andrew Bond from the University of Cambridge for XRD measurement and analysis. article_number: e202300128 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Nadia L. full_name: Farag, Nadia L. last_name: Farag - first_name: Rajesh B full_name: Jethwa, Rajesh B id: 4cc538d5-803f-11ed-ab7e-8139573aad8f last_name: Jethwa orcid: 0000-0002-0404-4356 - first_name: Alice E. full_name: Beardmore, Alice E. last_name: Beardmore - first_name: Teresa full_name: Insinna, Teresa last_name: Insinna - first_name: Christopher A. full_name: O'Keefe, Christopher A. last_name: O'Keefe - first_name: Peter A.A. full_name: Klusener, Peter A.A. last_name: Klusener - first_name: Clare P. full_name: Grey, Clare P. last_name: Grey - first_name: Dominic S. full_name: Wright, Dominic S. last_name: Wright citation: ama: Farag NL, Jethwa RB, Beardmore AE, et al. Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. 2023;16(13). doi:10.1002/cssc.202300128 apa: Farag, N. L., Jethwa, R. B., Beardmore, A. E., Insinna, T., O’Keefe, C. A., Klusener, P. A. A., … Wright, D. S. (2023). Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.202300128 chicago: Farag, Nadia L., Rajesh B Jethwa, Alice E. Beardmore, Teresa Insinna, Christopher A. O’Keefe, Peter A.A. Klusener, Clare P. Grey, and Dominic S. Wright. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem. Wiley, 2023. https://doi.org/10.1002/cssc.202300128. ieee: N. L. Farag et al., “Triarylamines as catholytes in aqueous organic redox flow batteries,” ChemSusChem, vol. 16, no. 13. Wiley, 2023. ista: Farag NL, Jethwa RB, Beardmore AE, Insinna T, O’Keefe CA, Klusener PAA, Grey CP, Wright DS. 2023. Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. 16(13), e202300128. mla: Farag, Nadia L., et al. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” ChemSusChem, vol. 16, no. 13, e202300128, Wiley, 2023, doi:10.1002/cssc.202300128. short: N.L. Farag, R.B. Jethwa, A.E. Beardmore, T. Insinna, C.A. O’Keefe, P.A.A. Klusener, C.P. Grey, D.S. Wright, ChemSusChem 16 (2023). date_created: 2023-05-21T22:01:05Z date_published: 2023-07-06T00:00:00Z date_updated: 2023-11-14T11:28:23Z day: '06' ddc: - '540' department: - _id: StFr doi: 10.1002/cssc.202300128 external_id: isi: - '000985051300001' pmid: - '36970847' file: - access_level: open_access checksum: efa0713289995af83a2147b3e8e1d6a6 content_type: application/pdf creator: dernst date_created: 2023-11-14T11:27:16Z date_updated: 2023-11-14T11:27:16Z file_id: '14532' file_name: 2023_ChemSusChem_Farag.pdf file_size: 1168683 relation: main_file success: 1 file_date_updated: 2023-11-14T11:27:16Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '13' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: ChemSusChem publication_identifier: eissn: - 1864-564X issn: - 1864-5631 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Triarylamines as catholytes in aqueous organic redox flow batteries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2023' ... --- _id: '13119' abstract: - lang: eng text: A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order. acknowledgement: Open access funding provided by EPFL Lausanne.We acknowledge discussions with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance in the final stages of the experiment. We acknowledge funding from the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654). F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone Project P 35891-N). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Victor full_name: Helson, Victor last_name: Helson - first_name: Timo full_name: Zwettler, Timo last_name: Zwettler - first_name: Farokh full_name: Mivehvar, Farokh last_name: Mivehvar - first_name: Elvia full_name: Colella, Elvia last_name: Colella - first_name: Kevin Etienne Robert full_name: Roux, Kevin Etienne Robert id: 53f93ea2-803f-11ed-ab7e-b283135794ef last_name: Roux - first_name: Hideki full_name: Konishi, Hideki last_name: Konishi - first_name: Helmut full_name: Ritsch, Helmut last_name: Ritsch - first_name: Jean Philippe full_name: Brantut, Jean Philippe last_name: Brantut citation: ama: Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 2023;618:716-720. doi:10.1038/s41586-023-06018-3 apa: Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi, H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06018-3 chicago: Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06018-3. ieee: V. Helson et al., “Density-wave ordering in a unitary Fermi gas with photon-mediated interactions,” Nature, vol. 618. Springer Nature, pp. 716–720, 2023. ista: Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H, Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 618, 716–720. mla: Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” Nature, vol. 618, Springer Nature, 2023, pp. 716–20, doi:10.1038/s41586-023-06018-3. short: V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi, H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720. date_created: 2023-06-04T22:01:03Z date_published: 2023-06-22T00:00:00Z date_updated: 2023-11-14T13:02:50Z day: '22' ddc: - '530' department: - _id: GeKa doi: 10.1038/s41586-023-06018-3 external_id: isi: - '001001139300008' file: - access_level: open_access checksum: 4887a296e3b6f54e8c0b946cbfd24f49 content_type: application/pdf creator: dernst date_created: 2023-11-14T13:00:19Z date_updated: 2023-11-14T13:00:19Z file_id: '14534' file_name: 2023_Nature_Helson.pdf file_size: 8156497 relation: main_file success: 1 file_date_updated: 2023-11-14T13:00:19Z has_accepted_license: '1' intvolume: ' 618' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 716-720 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Density-wave ordering in a unitary Fermi gas with photon-mediated interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 618 year: '2023' ... --- _id: '12911' abstract: - lang: eng text: 'This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.' acknowledgement: "This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. The authors also thank J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. Finally, we acknowledge the high quality review done by the anonymous referee of our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813." article_number: '109963' article_processing_charge: No article_type: original author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 - first_name: Augusto full_name: Gerolin, Augusto last_name: Gerolin - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 2023;285(4). doi:10.1016/j.jfa.2023.109963 apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (2023). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.109963 chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.109963. ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” Journal of Functional Analysis, vol. 285, no. 4. Elsevier, 2023. ista: Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 285(4), 109963. mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” Journal of Functional Analysis, vol. 285, no. 4, 109963, Elsevier, 2023, doi:10.1016/j.jfa.2023.109963. short: D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis 285 (2023). date_created: 2023-05-07T22:01:02Z date_published: 2023-08-15T00:00:00Z date_updated: 2023-11-14T13:21:01Z day: '15' department: - _id: RoSe - _id: JaMa doi: 10.1016/j.jfa.2023.109963 ec_funded: 1 external_id: arxiv: - '2106.11217' isi: - '000990804300001' intvolume: ' 285' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2106.11217 month: '08' oa: 1 oa_version: Preprint project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: ' F06504' name: Taming Complexity in Partial Di erential Systems publication: Journal of Functional Analysis publication_identifier: eissn: - 1096-0783 issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '9792' relation: earlier_version status: public scopus_import: '1' status: public title: A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 285 year: '2023' ... --- _id: '13177' abstract: - lang: eng text: In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established. acknowledgement: The second author was supported by the priority program SPP2026 of the German Research Foundation (DFG). The fourth author was supported by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the German Research Foundation (DFG) via RTG 1523/2. article_processing_charge: No article_type: original author: - first_name: Bobo full_name: Hua, Bobo last_name: Hua - first_name: Matthias full_name: Keller, Matthias last_name: Keller - first_name: Michael full_name: Schwarz, Michael last_name: Schwarz - first_name: Melchior full_name: Wirth, Melchior id: 88644358-0A0E-11EA-8FA5-49A33DDC885E last_name: Wirth orcid: 0000-0002-0519-4241 citation: ama: Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 2023;151(8):3401-3414. doi:10.1090/proc/14361 apa: Hua, B., Keller, M., Schwarz, M., & Wirth, M. (2023). Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/14361 chicago: Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/14361. ieee: B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and eigenvalue growth on graphs with finite measure,” Proceedings of the American Mathematical Society, vol. 151, no. 8. American Mathematical Society, pp. 3401–3414, 2023. ista: Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 151(8), 3401–3414. mla: Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society, vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:10.1090/proc/14361. short: B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical Society 151 (2023) 3401–3414. date_created: 2023-07-02T22:00:43Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-11-14T13:07:09Z day: '01' department: - _id: JaMa doi: 10.1090/proc/14361 external_id: arxiv: - '1804.08353' isi: - '000988204400001' intvolume: ' 151' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1804.08353' month: '08' oa: 1 oa_version: Preprint page: 3401-3414 publication: Proceedings of the American Mathematical Society publication_identifier: eissn: - 1088-6826 issn: - 0002-9939 publication_status: published publisher: American Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Sobolev-type inequalities and eigenvalue growth on graphs with finite measure type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 151 year: '2023' ... --- _id: '14554' abstract: - lang: eng text: 'The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format.' acknowledgement: "The authors thank the anonymous referees for their careful reading of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered the first part of this project)." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Federico full_name: Cornalba, Federico id: 2CEB641C-A400-11E9-A717-D712E6697425 last_name: Cornalba orcid: 0000-0002-6269-5149 - first_name: Tony full_name: Shardlow, Tony last_name: Shardlow citation: ama: 'Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 2023;57(5):3061-3090. doi:10.1051/m2an/2023077' apa: 'Cornalba, F., & Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2023077' chicago: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2023. https://doi.org/10.1051/m2an/2023077.' ieee: 'F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime,” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5. EDP Sciences, pp. 3061–3090, 2023.' ista: 'Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.' mla: 'Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5, EDP Sciences, 2023, pp. 3061–90, doi:10.1051/m2an/2023077.' short: 'F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.' date_created: 2023-11-19T23:00:55Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-11-20T08:38:47Z day: '01' ddc: - '510' department: - _id: JuFi doi: 10.1051/m2an/2023077 ec_funded: 1 file: - access_level: open_access checksum: 3aef1475b1882c8dec112df9a5167c39 content_type: application/pdf creator: dernst date_created: 2023-11-20T08:34:57Z date_updated: 2023-11-20T08:34:57Z file_id: '14560' file_name: 2023_ESAIM_Cornalba.pdf file_size: 1508534 relation: main_file success: 1 file_date_updated: 2023-11-20T08:34:57Z has_accepted_license: '1' intvolume: ' 57' issue: '5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 3061-3090 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 'ESAIM: Mathematical Modelling and Numerical Analysis' publication_identifier: eissn: - 2804-7214 issn: - 2822-7840 publication_status: published publisher: EDP Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/tonyshardlow/RIDK-FD scopus_import: '1' status: public title: 'The regularised inertial Dean'' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2023' ... --- _id: '14556' abstract: - lang: eng text: Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach. acknowledgement: 'We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.' article_number: '14242' article_processing_charge: No article_type: review author: - first_name: Emma L. full_name: Berdan, Emma L. last_name: Berdan - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Roger full_name: Butlin, Roger last_name: Butlin - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Inês full_name: Fragata, Inês last_name: Fragata - first_name: Kimberly J. full_name: Gilbert, Kimberly J. last_name: Gilbert - first_name: Paul full_name: Jay, Paul last_name: Jay - first_name: Martin full_name: Kapun, Martin last_name: Kapun - first_name: Katie E. full_name: Lotterhos, Katie E. last_name: Lotterhos - first_name: Claire full_name: Mérot, Claire last_name: Mérot - first_name: Esra full_name: Durmaz Mitchell, Esra last_name: Durmaz Mitchell - first_name: Marta full_name: Pascual, Marta last_name: Pascual - first_name: Catherine L. full_name: Peichel, Catherine L. last_name: Peichel - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Stephen W. full_name: Schaeffer, Stephen W. last_name: Schaeffer - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Thomas full_name: Flatt, Thomas last_name: Flatt citation: ama: Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242 apa: Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242 chicago: Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023. https://doi.org/10.1111/jeb.14242. ieee: E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology. Wiley, 2023. ista: Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242. mla: Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242. short: E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023). date_created: 2023-11-19T23:00:55Z date_published: 2023-11-08T00:00:00Z date_updated: 2023-11-20T08:51:09Z day: '08' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.14242 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jeb.14242 month: '11' oa: 1 oa_version: Published Version publication: Journal of Evolutionary Biology publication_identifier: eissn: - 1420-9101 issn: - 1010-061X publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: How chromosomal inversions reorient the evolutionary process tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14555' abstract: - lang: eng text: The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems. acknowledgement: The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article. article_number: '1287420' article_processing_charge: Yes article_type: original author: - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 2023;11. doi:10.3389/fcell.2023.1287420 apa: Riedl, M., & Sixt, M. K. (2023). The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2023.1287420 chicago: Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology. Frontiers, 2023. https://doi.org/10.3389/fcell.2023.1287420. ieee: M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction,” Frontiers in Cell and Developmental Biology, vol. 11. Frontiers, 2023. ista: Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11, 1287420. mla: Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology, vol. 11, 1287420, Frontiers, 2023, doi:10.3389/fcell.2023.1287420. short: M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023). date_created: 2023-11-19T23:00:55Z date_published: 2023-10-31T00:00:00Z date_updated: 2023-11-20T08:44:17Z day: '31' ddc: - '570' department: - _id: MiSi doi: 10.3389/fcell.2023.1287420 file: - access_level: open_access checksum: 61857fc3ebf019354932e7ee684658ce content_type: application/pdf creator: dernst date_created: 2023-11-20T08:41:15Z date_updated: 2023-11-20T08:41:15Z file_id: '14561' file_name: 2023_FrontiersCellDevBio_Riedl.pdf file_size: 2047622 relation: main_file success: 1 file_date_updated: 2023-11-20T08:41:15Z has_accepted_license: '1' intvolume: ' 11' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Frontiers in Cell and Developmental Biology publication_identifier: eissn: - 2296-634X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2023' ... --- _id: '14543' abstract: - lang: eng text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders. article_number: awad380 article_processing_charge: No article_type: original author: - first_name: Rauan full_name: Kaiyrzhanov, Rauan last_name: Kaiyrzhanov - first_name: Aboulfazl full_name: Rad, Aboulfazl last_name: Rad - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Aida full_name: Bertoli-Avella, Aida last_name: Bertoli-Avella - first_name: Wouter W full_name: Kallemeijn, Wouter W last_name: Kallemeijn - first_name: Annie full_name: Godwin, Annie last_name: Godwin - first_name: Maha S full_name: Zaki, Maha S last_name: Zaki - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Tracy full_name: Lau, Tracy last_name: Lau - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Stephanie full_name: Efthymiou, Stephanie last_name: Efthymiou - first_name: Ehsan full_name: Ghayoor Karimiani, Ehsan last_name: Ghayoor Karimiani - first_name: Maja full_name: Hempel, Maja last_name: Hempel - first_name: Elizabeth A full_name: Normand, Elizabeth A last_name: Normand - first_name: Sabine full_name: Rudnik-Schöneborn, Sabine last_name: Rudnik-Schöneborn - first_name: Ulrich A full_name: Schatz, Ulrich A last_name: Schatz - first_name: Marc P full_name: Baggelaar, Marc P last_name: Baggelaar - first_name: Muhammad full_name: Ilyas, Muhammad last_name: Ilyas - first_name: Tipu full_name: Sultan, Tipu last_name: Sultan - first_name: Javeria Raza full_name: Alvi, Javeria Raza last_name: Alvi - first_name: Manizha full_name: Ganieva, Manizha last_name: Ganieva - first_name: Ben full_name: Fowler, Ben last_name: Fowler - first_name: Ruxandra full_name: Aanicai, Ruxandra last_name: Aanicai - first_name: Gulsen full_name: Akay Tayfun, Gulsen last_name: Akay Tayfun - first_name: Abdulaziz full_name: Al Saman, Abdulaziz last_name: Al Saman - first_name: Abdulrahman full_name: Alswaid, Abdulrahman last_name: Alswaid - first_name: Nafise full_name: Amiri, Nafise last_name: Amiri - first_name: Nilufar full_name: Asilova, Nilufar last_name: Asilova - first_name: Vorasuk full_name: Shotelersuk, Vorasuk last_name: Shotelersuk - first_name: Patra full_name: Yeetong, Patra last_name: Yeetong - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Meisam full_name: Babaei, Meisam last_name: Babaei - first_name: Gholamreza full_name: Bahrami Monajemi, Gholamreza last_name: Bahrami Monajemi - first_name: Pouria full_name: Mohammadi, Pouria last_name: Mohammadi - first_name: Saeed full_name: Samie, Saeed last_name: Samie - first_name: Selina Husna full_name: Banu, Selina Husna last_name: Banu - first_name: Jorge Pinto full_name: Basto, Jorge Pinto last_name: Basto - first_name: Fanny full_name: Kortüm, Fanny last_name: Kortüm - first_name: Mislen full_name: Bauer, Mislen last_name: Bauer - first_name: Peter full_name: Bauer, Peter last_name: Bauer - first_name: Christian full_name: Beetz, Christian last_name: Beetz - first_name: Masoud full_name: Garshasbi, Masoud last_name: Garshasbi - first_name: Awatif full_name: Hameed Issa, Awatif last_name: Hameed Issa - first_name: Wafaa full_name: Eyaid, Wafaa last_name: Eyaid - first_name: Hind full_name: Ahmed, Hind last_name: Ahmed - first_name: Narges full_name: Hashemi, Narges last_name: Hashemi - first_name: Kazem full_name: Hassanpour, Kazem last_name: Hassanpour - first_name: Isabella full_name: Herman, Isabella last_name: Herman - first_name: Sherozjon full_name: Ibrohimov, Sherozjon last_name: Ibrohimov - first_name: Ban A full_name: Abdul-Majeed, Ban A last_name: Abdul-Majeed - first_name: Maria full_name: Imdad, Maria last_name: Imdad - first_name: Maksudjon full_name: Isrofilov, Maksudjon last_name: Isrofilov - first_name: Qassem full_name: Kaiyal, Qassem last_name: Kaiyal - first_name: Suliman full_name: Khan, Suliman last_name: Khan - first_name: Brian full_name: Kirmse, Brian last_name: Kirmse - first_name: Janet full_name: Koster, Janet last_name: Koster - first_name: Charles Marques full_name: Lourenço, Charles Marques last_name: Lourenço - first_name: Tadahiro full_name: Mitani, Tadahiro last_name: Mitani - first_name: Oana full_name: Moldovan, Oana last_name: Moldovan - first_name: David full_name: Murphy, David last_name: Murphy - first_name: Maryam full_name: Najafi, Maryam last_name: Najafi - first_name: Davut full_name: Pehlivan, Davut last_name: Pehlivan - first_name: Maria Eugenia full_name: Rocha, Maria Eugenia last_name: Rocha - first_name: Vincenzo full_name: Salpietro, Vincenzo last_name: Salpietro - first_name: Miriam full_name: Schmidts, Miriam last_name: Schmidts - first_name: Adel full_name: Shalata, Adel last_name: Shalata - first_name: Mohammad full_name: Mahroum, Mohammad last_name: Mahroum - first_name: Jawabreh Kassem full_name: Talbeya, Jawabreh Kassem last_name: Talbeya - first_name: Robert W full_name: Taylor, Robert W last_name: Taylor - first_name: Dayana full_name: Vazquez, Dayana last_name: Vazquez - first_name: Annalisa full_name: Vetro, Annalisa last_name: Vetro - first_name: Hans R full_name: Waterham, Hans R last_name: Waterham - first_name: Mashaya full_name: Zaman, Mashaya last_name: Zaman - first_name: Tina A full_name: Schrader, Tina A last_name: Schrader - first_name: Wendy K full_name: Chung, Wendy K last_name: Chung - first_name: Renzo full_name: Guerrini, Renzo last_name: Guerrini - first_name: James R full_name: Lupski, James R last_name: Lupski - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson - first_name: Mohnish full_name: Suri, Mohnish last_name: Suri - first_name: Yalda full_name: Jamshidi, Yalda last_name: Jamshidi - first_name: Kailash P full_name: Bhatia, Kailash P last_name: Bhatia - first_name: Barbara full_name: Vona, Barbara last_name: Vona - first_name: Michael full_name: Schrader, Michael last_name: Schrader - first_name: Mariasavina full_name: Severino, Mariasavina last_name: Severino - first_name: Matthew full_name: Guille, Matthew last_name: Guille - first_name: Edward W full_name: Tate, Edward W last_name: Tate - first_name: Gaurav K full_name: Varshney, Gaurav K last_name: Varshney - first_name: Henry full_name: Houlden, Henry last_name: Houlden - first_name: Reza full_name: Maroofian, Reza last_name: Maroofian citation: ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2023. doi:10.1093/brain/awad380 apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380 chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2023. https://doi.org/10.1093/brain/awad380. ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain. Oxford University Press, 2023. ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain., awad380. mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, awad380, Oxford University Press, 2023, doi:10.1093/brain/awad380. short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023). date_created: 2023-11-16T12:36:51Z date_published: 2023-11-10T00:00:00Z date_updated: 2023-11-20T10:17:32Z day: '10' department: - _id: GradSch doi: 10.1093/brain/awad380 extern: '1' keyword: - Neurology (clinical) language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/brain/awad380 month: '11' oa: 1 oa_version: Submitted Version publication: Brain publication_identifier: eissn: - 1460-2156 issn: - 0006-8950 publication_status: epub_ahead publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14542' abstract: - lang: eng text: "It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit." acknowledgement: We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427. article_number: '2360005 ' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 - first_name: Barbara full_name: Roos, Barbara id: 5DA90512-D80F-11E9-8994-2E2EE6697425 last_name: Roos orcid: 0000-0002-9071-5880 citation: ama: Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x apa: Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/s0129055x2360005x chicago: Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x. ieee: S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing, 2023. ista: Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005. mla: Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics, 2360005, World Scientific Publishing, 2023, doi:10.1142/s0129055x2360005x. short: S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023). date_created: 2023-11-15T23:48:14Z date_published: 2023-10-31T00:00:00Z date_updated: 2023-11-20T10:04:38Z day: '31' department: - _id: GradSch - _id: LaEr - _id: RoSe doi: 10.1142/s0129055x2360005x ec_funded: 1 external_id: arxiv: - '2301.05621' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1142/S0129055X2360005X month: '10' oa: 1 oa_version: Published Version project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity publication: Reviews in Mathematical Physics publication_identifier: eissn: - 1793-6659 issn: - 0129-055X publication_status: epub_ahead publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: Universality in low-dimensional BCS theory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14553' abstract: - lang: eng text: Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method. article_number: '042430' article_processing_charge: No article_type: original author: - first_name: Ekaterina full_name: Fedotova, Ekaterina id: c1bea5e1-878e-11ee-9dff-d7404e4422ab last_name: Fedotova orcid: 0000-0001-7242-015X - first_name: Nikolai full_name: Kuznetsov, Nikolai last_name: Kuznetsov - first_name: Egor full_name: Tiunov, Egor last_name: Tiunov - first_name: A. E. full_name: Ulanov, A. E. last_name: Ulanov - first_name: A. I. full_name: Lvovsky, A. I. last_name: Lvovsky citation: ama: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 2023;108(4). doi:10.1103/PhysRevA.108.042430 apa: Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., & Lvovsky, A. I. (2023). Continuous-variable quantum tomography of high-amplitude states. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.108.042430 chicago: Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.108.042430. ieee: E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable quantum tomography of high-amplitude states,” Physical Review A, vol. 108, no. 4. American Physical Society, 2023. ista: Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430. mla: Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A, vol. 108, no. 4, 042430, American Physical Society, 2023, doi:10.1103/PhysRevA.108.042430. short: E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023). date_created: 2023-11-19T23:00:54Z date_published: 2023-10-30T00:00:00Z date_updated: 2023-11-20T10:26:51Z day: '30' department: - _id: JoFi doi: 10.1103/PhysRevA.108.042430 external_id: arxiv: - '2212.07406' intvolume: ' 108' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2212.07406 month: '10' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Continuous-variable quantum tomography of high-amplitude states type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '14551' abstract: - lang: eng text: Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale. acknowledgement: We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Amy full_name: Briffa, Amy last_name: Briffa - first_name: Elizabeth full_name: Hollwey, Elizabeth id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd last_name: Hollwey - first_name: Zaigham full_name: Shahzad, Zaigham last_name: Shahzad - first_name: Jonathan D. full_name: Moore, Jonathan D. last_name: Moore - first_name: David B. full_name: Lyons, David B. last_name: Lyons - first_name: Martin full_name: Howard, Martin last_name: Howard - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007 apa: Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., & Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier. https://doi.org/10.1016/j.cels.2023.10.007 chicago: Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007. ieee: A. Briffa et al., “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems, vol. 14, no. 11. Elsevier, pp. 953–967, 2023. ista: Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967. mla: Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007. short: A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967. date_created: 2023-11-19T23:00:54Z date_published: 2023-11-15T00:00:00Z date_updated: 2023-11-20T11:24:34Z day: '15' ddc: - '570' department: - _id: DaZi doi: 10.1016/j.cels.2023.10.007 ec_funded: 1 external_id: pmid: - '37944515' file: - access_level: open_access checksum: 101fdac59e6f1102d68ef91f2b5bd51a content_type: application/pdf creator: dernst date_created: 2023-11-20T11:22:52Z date_updated: 2023-11-20T11:22:52Z file_id: '14580' file_name: 2023_CellSystems_Briffa.pdf file_size: 5587897 relation: main_file success: 1 file_date_updated: 2023-11-20T11:22:52Z has_accepted_license: '1' intvolume: ' 14' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 953-967 pmid: 1 project: - _id: 62935a00-2b32-11ec-9570-eff30fa39068 call_identifier: H2020 grant_number: '725746' name: Quantitative analysis of DNA methylation maintenance with chromatin publication: Cell Systems publication_identifier: eissn: - 2405-4720 issn: - 2405-4712 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14579' abstract: - lang: eng text: "This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n" article_processing_charge: No author: - first_name: William full_name: Wetzel, William last_name: Wetzel citation: ama: 'Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117' apa: 'Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/10.5281/ZENODO.8133117' chicago: 'Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.' ieee: 'W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.' ista: 'Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117.' mla: 'Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117.' short: W. Wetzel, (2023). date_created: 2023-11-20T11:07:45Z date_published: 2023-07-11T00:00:00Z date_updated: 2023-11-20T11:17:33Z day: '11' ddc: - '570' department: - _id: NiBa doi: 10.5281/ZENODO.8133117 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8133118 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14552' relation: used_in_publication status: public status: public title: 'HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12334' abstract: - lang: eng text: Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R." article_number: add6495 article_processing_charge: No article_type: original author: - first_name: Florian full_name: Fäßler, Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - first_name: Manjunath full_name: Javoor, Manjunath id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2 last_name: Javoor - first_name: Julia full_name: Datler, Julia id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87 last_name: Datler orcid: 0000-0002-3616-8580 - first_name: Hermann full_name: Döring, Hermann last_name: Döring - first_name: Florian full_name: Hofer, Florian id: b9d234ba-9e33-11ed-95b6-cd561df280e6 last_name: Hofer - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 2023;9(3). doi:10.1126/sciadv.add6495 apa: Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495 chicago: Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495. ieee: F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023. ista: Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495. mla: Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495. short: F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023). date_created: 2023-01-23T07:26:42Z date_published: 2023-01-20T00:00:00Z date_updated: 2023-11-21T08:05:35Z day: '20' ddc: - '570' department: - _id: FlSc - _id: EM-Fac doi: 10.1126/sciadv.add6495 external_id: isi: - '000964550100015' file: - access_level: open_access checksum: ce81a6d0b84170e5e8c62f6acfa15d9e content_type: application/pdf creator: dernst date_created: 2023-01-23T07:45:54Z date_updated: 2023-01-23T07:45:54Z file_id: '12335' file_name: 2023_ScienceAdvances_Faessler.pdf file_size: 1756234 relation: main_file success: 1 file_date_updated: 2023-01-23T07:45:54Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '3' keyword: - Multidisciplinary language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: record: - id: '14562' relation: research_data status: public scopus_import: '1' status: public title: ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2023' ... --- _id: '14562' abstract: - lang: eng text: "Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n" acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: ScienComp - _id: EM-Fac acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R." article_processing_charge: No author: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562 apa: Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562 chicago: Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562. ieee: F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023. ista: Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562. mla: Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562. short: F.K. Schur, (2023). contributor: - contributor_type: researcher first_name: Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - contributor_type: researcher first_name: Manjunath id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2 last_name: Javoor - contributor_type: researcher first_name: Julia id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87 last_name: Datler orcid: 0000-0002-3616-8580 - contributor_type: researcher first_name: Hermann last_name: Döring - contributor_type: researcher first_name: Florian id: b9d234ba-9e33-11ed-95b6-cd561df280e6 last_name: Hofer - contributor_type: researcher first_name: Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - contributor_type: researcher first_name: Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - contributor_type: researcher first_name: Jan last_name: Faix - contributor_type: researcher first_name: Klemens last_name: Rottner - contributor_type: researcher first_name: Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 date_created: 2023-11-20T09:22:33Z date_published: 2023-11-21T00:00:00Z date_updated: 2023-11-21T08:05:34Z day: '21' ddc: - '570' department: - _id: FlSc doi: 10.15479/AT:ISTA:14562 file: - access_level: open_access checksum: e9bab797b44614f144a5b02d9636f8c3 content_type: application/zip creator: fschur date_created: 2023-11-20T10:27:17Z date_updated: 2023-11-20T10:27:17Z file_id: '14570' file_name: Figure2.zip file_size: 1581687449 relation: main_file success: 1 - access_level: open_access checksum: 4efd388cccd03c549fc90f6e46d37006 content_type: application/zip creator: fschur date_created: 2023-11-20T10:29:18Z date_updated: 2023-11-20T10:29:18Z file_id: '14571' file_name: SupplementaryFigure3.zip file_size: 116088565 relation: main_file success: 1 - access_level: open_access checksum: bdeb232dc94d0c22a3f7e0d18189ce89 content_type: application/zip creator: fschur date_created: 2023-11-20T10:44:39Z date_updated: 2023-11-20T10:44:39Z file_id: '14572' file_name: Figure5.zip file_size: 5154614201 relation: main_file success: 1 - access_level: open_access checksum: 83aee17d621a05d865f68f39c8892d27 content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:00Z date_updated: 2023-11-20T10:46:00Z file_id: '14573' file_name: SupplementaryFigure7.zip file_size: 1277893286 relation: main_file success: 1 - access_level: open_access checksum: fb9beb6fe15c8dac6679dd02044d2ea6 content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:08Z date_updated: 2023-11-20T10:46:08Z file_id: '14574' file_name: SupplementaryFigure9.zip file_size: 228485124 relation: main_file success: 1 - access_level: open_access checksum: 4f3644e5feabe4824486d56885bb79fe content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:32Z date_updated: 2023-11-20T10:46:32Z file_id: '14575' file_name: SupplementaryFigure10.zip file_size: 1226788198 relation: main_file success: 1 - access_level: open_access checksum: 96167f722ed0ca78e30681cd1573b9d7 content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:17Z date_updated: 2023-11-20T10:46:17Z file_id: '14576' file_name: SupplementaryFigure11.zip file_size: 277577131 relation: main_file success: 1 - access_level: open_access checksum: d1e03c9805c18cfbc2e9fdf38a9f556f content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:29Z date_updated: 2023-11-20T10:46:29Z file_id: '14577' file_name: SupplementaryFigure15.zip file_size: 591483468 relation: main_file success: 1 - access_level: open_access checksum: 4d437c04fdb3c1e699618063c4bd21c3 content_type: application/zip creator: fschur date_created: 2023-11-20T10:47:00Z date_updated: 2023-11-20T10:47:00Z file_id: '14578' file_name: SupplementaryFigure17.zip file_size: 1709528579 relation: main_file success: 1 - access_level: open_access checksum: 967b5378a4f16c43f490eae328afe50e content_type: application/zip creator: fschur date_created: 2023-11-20T11:26:36Z date_updated: 2023-11-20T11:26:36Z file_id: '14581' file_name: SupplementaryFigure4.zip file_size: 1920765280 relation: main_file success: 1 - access_level: open_access checksum: 11899986cf0b471d258fe168ee33a3ea content_type: application/zip creator: fschur date_created: 2023-11-20T11:38:12Z date_updated: 2023-11-20T11:38:12Z file_id: '14583' file_name: Figure1_partA.zip file_size: 3013566196 relation: main_file success: 1 - access_level: open_access checksum: c452afe1ab506d58d32e601d5b3878bb content_type: application/zip creator: fschur date_created: 2023-11-20T11:43:23Z date_updated: 2023-11-20T11:43:23Z file_id: '14584' file_name: Figure1_partB.zip file_size: 3250260203 relation: main_file success: 1 - access_level: open_access checksum: 223c98eceecbe65dd268f4f363a620d8 content_type: text/rtf creator: fschur date_created: 2023-11-20T11:49:58Z date_updated: 2023-11-20T11:49:58Z file_id: '14585' file_name: ReadMe.rtf file_size: 1460 relation: main_file success: 1 file_date_updated: 2023-11-20T11:49:58Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '11' oa: 1 oa_version: Published Version project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex publisher: Institute of Science and Technology Austria related_material: record: - id: '12334' relation: used_in_publication status: public status: public title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning" tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14502' abstract: - lang: eng text: A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner. author: - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Behnam full_name: Amiri, Behnam last_name: Amiri - first_name: Florian full_name: Fäßler, Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - first_name: Martin full_name: Falcke, Martin last_name: Falcke - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:10.15479/AT:ISTA:14502 apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502 chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14502. ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023. ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502. mla: Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14502. short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023). date_created: 2023-11-08T19:40:54Z date_published: 2023-11-21T00:00:00Z date_updated: 2023-11-21T08:36:02Z day: '21' ddc: - '570' department: - _id: FlSc doi: 10.15479/AT:ISTA:14502 file: - access_level: open_access checksum: a8b9adeb53a4109dea4d5e39fa1acccf content_type: application/zip creator: fschur date_created: 2023-11-08T20:23:07Z date_updated: 2023-11-08T20:23:07Z file_id: '14503' file_name: Computational_Toolbox_v1.2.zip file_size: 347641117 relation: main_file success: 1 - access_level: open_access checksum: 14db2addbfca61a085ba301ed6f2900b content_type: text/plain creator: dernst date_created: 2023-11-21T08:20:23Z date_updated: 2023-11-21T08:20:23Z file_id: '14586' file_name: Readme.txt file_size: 1522 relation: main_file success: 1 file_date_updated: 2023-11-21T08:20:23Z has_accepted_license: '1' keyword: - cryo-electron tomography - actin cytoskeleton - toolbox license: https://choosealicense.com/licenses/agpl-3.0/ month: '11' oa: 1 project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex publisher: Institute of Science and Technology Austria related_material: record: - id: '10290' relation: used_for_analysis_in status: public status: public title: Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data tmp: legal_code_url: https://www.gnu.org/licenses/agpl-3.0.html name: GNU Affero General Public License v3.0 short: 'GNU AGPLv3 ' type: software user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13342' abstract: - lang: eng text: Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease. acknowledgement: We thank Christoph Mayr and Bingzhi Wang for initial experiments on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry, EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support. This study was supported by the Peter Hans Hofschneider Professorship of the foundation “Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to JR), and the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled and organized by Projekt DEAL. article_number: e114557 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Janina full_name: Kroll, Janina last_name: Kroll - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Arthur full_name: Kuznetcov, Arthur last_name: Kuznetcov - first_name: Kasia full_name: Stefanowski, Kasia last_name: Stefanowski - first_name: Monika D. full_name: Hermann, Monika D. last_name: Hermann - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Lubuna B full_name: Shafeek, Lubuna B id: 3CD37A82-F248-11E8-B48F-1D18A9856A87 last_name: Shafeek orcid: 0000-0001-7180-6050 - first_name: Annette full_name: Müller-Taubenberger, Annette last_name: Müller-Taubenberger - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 citation: ama: Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557 apa: Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557 chicago: Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557. ieee: J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid migration,” EMBO Journal. Embo Press, 2023. ista: Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557. mla: Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557. short: J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin, L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023). date_created: 2023-08-01T08:59:06Z date_published: 2023-11-21T00:00:00Z date_updated: 2023-11-27T08:47:45Z day: '21' ddc: - '570' department: - _id: NanoFab - _id: Bio doi: 10.15252/embj.2023114557 external_id: pmid: - '37987147' file: - access_level: open_access checksum: 6261d0041c7e8d284c39712c40079730 content_type: application/pdf creator: dernst date_created: 2023-11-27T08:45:56Z date_updated: 2023-11-27T08:45:56Z file_id: '14611' file_name: 2023_EmboJournal_Kroll.pdf file_size: 4862497 relation: main_file success: 1 file_date_updated: 2023-11-27T08:45:56Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: EMBO Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Adaptive pathfinding by nucleokinesis during amoeboid migration tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14610' abstract: - lang: eng text: AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host. acknowledgement: "We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Claudio full_name: Bussi, Claudio last_name: Bussi - first_name: Agustín full_name: Mangiarotti, Agustín last_name: Mangiarotti - first_name: Christian Eduardo full_name: Vanhille-Campos, Christian Eduardo id: 3adeca52-9313-11ed-b1ac-c170b2505714 last_name: Vanhille-Campos - first_name: Beren full_name: Aylan, Beren last_name: Aylan - first_name: Enrica full_name: Pellegrino, Enrica last_name: Pellegrino - first_name: Natalia full_name: Athanasiadi, Natalia last_name: Athanasiadi - first_name: Antony full_name: Fearns, Antony last_name: Fearns - first_name: Angela full_name: Rodgers, Angela last_name: Rodgers - first_name: Titus M. full_name: Franzmann, Titus M. last_name: Franzmann - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Rumiana full_name: Dimova, Rumiana last_name: Dimova - first_name: Maximiliano G. full_name: Gutierrez, Maximiliano G. last_name: Gutierrez citation: ama: Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w apa: Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w chicago: Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w. ieee: C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal membranes,” Nature. Springer Nature, 2023. ista: Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. mla: Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w. short: C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature (2023). date_created: 2023-11-27T07:56:37Z date_published: 2023-11-15T00:00:00Z date_updated: 2023-11-27T09:05:08Z day: '15' department: - _id: AnSa doi: 10.1038/s41586-023-06726-w external_id: pmid: - '37968398' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41586-023-06726-w month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41586-023-06882-z record: - id: '14472' relation: research_data status: public status: public title: Stress granules plug and stabilize damaged endolysosomal membranes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14472' abstract: - lang: eng text: "Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w." article_processing_charge: No author: - first_name: Christian Eduardo full_name: Vanhille-Campos, Christian Eduardo id: 3adeca52-9313-11ed-b1ac-c170b2505714 last_name: Vanhille-Campos - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472 apa: Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472 chicago: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472. ieee: C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023. ista: Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472. mla: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472. short: C.E. Vanhille-Campos, A. Šarić, (2023). date_created: 2023-10-30T16:38:32Z date_published: 2023-10-31T00:00:00Z date_updated: 2023-11-27T09:05:07Z day: '31' ddc: - '570' department: - _id: AnSa doi: 10.15479/AT:ISTA:14472 file: - access_level: open_access checksum: a18706e952e8660c51ede52a167270b7 content_type: application/zip creator: ipalaia date_created: 2023-10-30T16:31:08Z date_updated: 2023-10-30T16:31:08Z file_id: '14473' file_name: SGporecondensation-main.zip file_size: 62821432 relation: main_file success: 1 - access_level: open_access checksum: 389eab31c6509dbc05795017fb618758 content_type: text/plain creator: dernst date_created: 2023-10-31T08:57:50Z date_updated: 2023-10-31T08:57:50Z file_id: '14474' file_name: README.txt file_size: 1697 relation: main_file success: 1 file_date_updated: 2023-10-31T08:57:50Z has_accepted_license: '1' month: '10' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14610' relation: used_in_publication status: public status: public title: Stress granules plug and stabilize damaged endolysosomal membranes tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12747' abstract: - lang: eng text: Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing. acknowledgement: 'The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.' article_processing_charge: No article_type: original author: - first_name: Domagoj full_name: Cikes, Domagoj last_name: Cikes - first_name: Kareem full_name: Elsayad, Kareem last_name: Elsayad - first_name: Erdinc full_name: Sezgin, Erdinc last_name: Sezgin - first_name: Erika full_name: Koitai, Erika last_name: Koitai - first_name: Torma full_name: Ferenc, Torma last_name: Ferenc - first_name: Michael full_name: Orthofer, Michael last_name: Orthofer - first_name: Rebecca full_name: Yarwood, Rebecca last_name: Yarwood - first_name: Leonhard X. full_name: Heinz, Leonhard X. last_name: Heinz - first_name: Vitaly full_name: Sedlyarov, Vitaly last_name: Sedlyarov - first_name: Nasser full_name: Darwish-Miranda, Nasser id: 39CD9926-F248-11E8-B48F-1D18A9856A87 last_name: Darwish-Miranda orcid: 0000-0002-8821-8236 - first_name: Adrian full_name: Taylor, Adrian last_name: Taylor - first_name: Sophie full_name: Grapentine, Sophie last_name: Grapentine - first_name: Fathiya full_name: al-Murshedi, Fathiya last_name: al-Murshedi - first_name: Anne full_name: Abot, Anne last_name: Abot - first_name: Adelheid full_name: Weidinger, Adelheid last_name: Weidinger - first_name: Candice full_name: Kutchukian, Candice last_name: Kutchukian - first_name: Colline full_name: Sanchez, Colline last_name: Sanchez - first_name: Shane J. F. full_name: Cronin, Shane J. F. last_name: Cronin - first_name: Maria full_name: Novatchkova, Maria last_name: Novatchkova - first_name: Anoop full_name: Kavirayani, Anoop last_name: Kavirayani - first_name: Thomas full_name: Schuetz, Thomas last_name: Schuetz - first_name: Bernhard full_name: Haubner, Bernhard last_name: Haubner - first_name: Lisa full_name: Haas, Lisa last_name: Haas - first_name: Astrid full_name: Hagelkruys, Astrid last_name: Hagelkruys - first_name: Suzanne full_name: Jackowski, Suzanne last_name: Jackowski - first_name: Andrey full_name: Kozlov, Andrey last_name: Kozlov - first_name: Vincent full_name: Jacquemond, Vincent last_name: Jacquemond - first_name: Claude full_name: Knauf, Claude last_name: Knauf - first_name: Giulio full_name: Superti-Furga, Giulio last_name: Superti-Furga - first_name: Eric full_name: Rullman, Eric last_name: Rullman - first_name: Thomas full_name: Gustafsson, Thomas last_name: Gustafsson - first_name: John full_name: McDermot, John last_name: McDermot - first_name: Martin full_name: Lowe, Martin last_name: Lowe - first_name: Zsolt full_name: Radak, Zsolt last_name: Radak - first_name: Jeffrey S. full_name: Chamberlain, Jeffrey S. last_name: Chamberlain - first_name: Marica full_name: Bakovic, Marica last_name: Bakovic - first_name: Siddharth full_name: Banka, Siddharth last_name: Banka - first_name: Josef M. full_name: Penninger, Josef M. last_name: Penninger citation: ama: Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515. doi:10.1038/s42255-023-00766-2 apa: Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2 chicago: Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature, 2023. https://doi.org/10.1038/s42255-023-00766-2. ieee: D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature, pp. 495–515, 2023. ista: Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515. mla: Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp. 495–515, doi:10.1038/s42255-023-00766-2. short: D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515. date_created: 2023-03-23T12:58:43Z date_published: 2023-03-20T00:00:00Z date_updated: 2023-11-28T07:31:33Z day: '20' department: - _id: Bio doi: 10.1038/s42255-023-00766-2 external_id: isi: - '000992064000002' pmid: - '36941451' intvolume: ' 5' isi: 1 keyword: - Cell Biology - Physiology (medical) - Endocrinology - Diabetes and Metabolism - Internal Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2022.03.02.482658 month: '03' oa: 1 oa_version: Preprint page: 495-515 pmid: 1 publication: Nature Metabolism publication_identifier: issn: - 2522-5812 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s42255-023-00791-1 scopus_import: '1' status: public title: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2023' ... --- _id: '14609' abstract: - lang: eng text: "Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art." acknowledgement: The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N. article_processing_charge: No author: - first_name: Sourav full_name: Das, Sourav last_name: Das - first_name: Zhuolun full_name: Xiang, Zhuolun last_name: Xiang - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Ling full_name: Ren, Ling last_name: Ren citation: ama: 'Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: 32nd USENIX Security Symposium. Vol 8. Usenix; 2023:5359-5376.' apa: 'Das, S., Xiang, Z., Kokoris Kogias, E., & Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In 32nd USENIX Security Symposium (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix.' chicago: Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In 32nd USENIX Security Symposium, 8:5359–76. Usenix, 2023. ieee: S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in 32nd USENIX Security Symposium, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376. ista: Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376. mla: Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” 32nd USENIX Security Symposium, vol. 8, Usenix, 2023, pp. 5359–76. short: S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376. conference: end_date: 2023-08-11 location: Anaheim, CA, United States name: USENIX Security Symposium start_date: 2023-08-09 date_created: 2023-11-26T23:00:55Z date_published: 2023-08-15T00:00:00Z date_updated: 2023-11-28T09:17:38Z day: '15' ddc: - '000' department: - _id: ElKo file: - access_level: open_access checksum: 1a730765930138e23c6efd2575872641 content_type: application/pdf creator: dernst date_created: 2023-11-28T09:14:34Z date_updated: 2023-11-28T09:14:34Z file_id: '14621' file_name: 2023_USENIX_Das.pdf file_size: 704331 relation: main_file success: 1 file_date_updated: 2023-11-28T09:14:34Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2022/1389 month: '08' oa: 1 oa_version: Published Version page: 5359-5376 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Secure Network and Hardware for Efficient Blockchains publication: 32nd USENIX Security Symposium publication_identifier: isbn: - '9781713879497' publication_status: published publisher: Usenix quality_controlled: '1' scopus_import: '1' status: public title: Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2023' ... --- _id: '14603' abstract: - lang: eng text: Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances. acknowledgement: A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability. article_number: '184110' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Aleks full_name: Reinhardt, Aleks last_name: Reinhardt - first_name: Pin Yu full_name: Chew, Pin Yu last_name: Chew - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 2023;159(18). doi:10.1063/5.0173341 apa: Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341 chicago: Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341. ieee: A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” Journal of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023. ista: Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110. mla: Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341. short: A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023). date_created: 2023-11-26T23:00:54Z date_published: 2023-11-14T00:00:00Z date_updated: 2023-11-28T08:39:23Z day: '14' ddc: - '530' - '540' department: - _id: BiCh doi: 10.1063/5.0173341 external_id: arxiv: - '2308.10886' file: - access_level: open_access checksum: f668ee0d07096eef81159d05bc27aabc content_type: application/pdf creator: dernst date_created: 2023-11-28T08:39:06Z date_updated: 2023-11-28T08:39:06Z file_id: '14620' file_name: 2023_JourChemicalPhysics_Reinhardt.pdf file_size: 6276059 relation: main_file success: 1 file_date_updated: 2023-11-28T08:39:06Z has_accepted_license: '1' intvolume: ' 159' issue: '18' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: record: - id: '14619' relation: research_data status: public scopus_import: '1' status: public title: A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2023' ... --- _id: '14604' abstract: - lang: eng text: Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. acknowledgement: All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169 apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169 chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpad169. ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023. ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511. mla: Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169. short: M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511. date_created: 2023-11-26T23:00:54Z date_published: 2023-11-02T00:00:00Z date_updated: 2023-11-28T08:25:28Z day: '02' ddc: - '570' department: - _id: BeVi doi: 10.1093/evolut/qpad169 external_id: pmid: - '37738212' file: - access_level: open_access checksum: b66dc10edae92d38918d534e64dda77c content_type: application/pdf creator: dernst date_created: 2023-11-28T08:12:15Z date_updated: 2023-11-28T08:12:15Z file_id: '14618' file_name: 2023_Evolution_Toups.pdf file_size: 1399102 relation: main_file success: 1 file_date_updated: 2023-11-28T08:12:15Z has_accepted_license: '1' intvolume: ' 77' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 2504-2511 pmid: 1 publication: Evolution publication_identifier: eissn: - 1558-5646 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://git.ista.ac.at/bvicoso/veryoldx record: - id: '14616' relation: research_data status: public - id: '14617' relation: research_data status: public scopus_import: '1' status: public title: The X chromosome of insects likely predates the origin of class Insecta tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2023' ... --- _id: '14616' abstract: - lang: eng text: Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. article_processing_charge: No author: - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5061/DRYAD.HX3FFBGKT apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT. ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023. ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT. mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT. short: M.A. Toups, B. Vicoso, (2023). date_created: 2023-11-28T08:01:53Z date_published: 2023-09-15T00:00:00Z date_updated: 2023-11-28T08:17:31Z day: '15' ddc: - '570' department: - _id: BeVi doi: 10.5061/DRYAD.HX3FFBGKT has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.hx3ffbgkt month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '14604' relation: used_in_publication status: public status: public title: The X chromosome of insects likely predates the origin of Class Insecta tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14617' abstract: - lang: eng text: Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. article_processing_charge: No author: - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5281/ZENODO.8138705 apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705 chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705. ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023. ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705. mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705. short: M.A. Toups, B. Vicoso, (2023). date_created: 2023-11-28T08:04:03Z date_published: 2023-09-15T00:00:00Z date_updated: 2023-11-28T08:25:28Z day: '15' ddc: - '570' department: - _id: BeVi doi: 10.5281/ZENODO.8138705 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8138705 month: '09' oa: 1 oa_version: Published Version other_data_license: MIT License publisher: Zenodo related_material: record: - id: '14604' relation: used_in_publication status: public status: public title: The X chromosome of insects likely predates the origin of Class Insecta type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14619' abstract: - lang: eng text: Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341). article_processing_charge: No author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: 'Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094' apa: 'Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094' chicago: 'Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.' ieee: 'B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.' ista: 'Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.' mla: 'Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.' short: B. Cheng, (2023). date_created: 2023-11-28T08:32:18Z date_published: 2023-10-02T00:00:00Z date_updated: 2023-11-28T08:39:22Z day: '02' ddc: - '530' department: - _id: BiCh doi: 10.5281/ZENODO.8398094 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8398094 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14603' relation: used_in_publication status: public status: public title: 'BingqingCheng/solubility: V1.0' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14564' abstract: - lang: eng text: Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized. acknowledgement: The research of B.K. is supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020). This research was conducted during the visits of P.M. Krishna to the Center for Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November 2018 to June 2019 and July 2019 and October 2019, respectively. The authors are very grateful to the three anonymous reviewers who provided very thoughtful and constructive comments during the review process that helped greatly improve and shape the final version of the manuscript. article_number: e2022MS003391 article_processing_charge: Yes article_type: original author: - first_name: B. full_name: Khouider, B. last_name: Khouider - first_name: BIDYUT B full_name: GOSWAMI, BIDYUT B id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b last_name: GOSWAMI orcid: 0000-0001-8602-3083 - first_name: R. full_name: Phani, R. last_name: Phani - first_name: A. J. full_name: Majda, A. J. last_name: Majda citation: ama: Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 2023;15(11). doi:10.1029/2022ms003391 apa: Khouider, B., GOSWAMI, B. B., Phani, R., & Majda, A. J. (2023). A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. American Geophysical Union. https://doi.org/10.1029/2022ms003391 chicago: Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems. American Geophysical Union, 2023. https://doi.org/10.1029/2022ms003391. ieee: B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11. American Geophysical Union, 2023. ista: Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391. mla: Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:10.1029/2022ms003391. short: B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023). date_created: 2023-11-20T09:18:21Z date_published: 2023-11-01T00:00:00Z date_updated: 2023-11-28T12:04:42Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1029/2022ms003391 file: - access_level: open_access checksum: e30329dd985559de0ddc7021ca7382b4 content_type: application/pdf creator: dernst date_created: 2023-11-20T11:29:16Z date_updated: 2023-11-20T11:29:16Z file_id: '14582' file_name: 2023_JAMES_Khoulder.pdf file_size: 6435697 relation: main_file success: 1 file_date_updated: 2023-11-20T11:29:16Z has_accepted_license: '1' intvolume: ' 15' issue: '11' keyword: - General Earth and Planetary Sciences - Environmental Chemistry - Global and Planetary Change language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Journal of Advances in Modeling Earth Systems publication_identifier: eissn: - 1942-2466 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '12789' abstract: - lang: eng text: Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior. acknowledged_ssus: - _id: M-Shop acknowledgement: This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile. article_number: '034901' article_processing_charge: No article_type: original author: - first_name: Nicolás full_name: Mujica, Nicolás last_name: Mujica - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901 apa: Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.034901 chicago: Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901. ieee: N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” Physical Review E, vol. 107, no. 3. American Physical Society, 2023. ista: Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901. mla: Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901. short: N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023). date_created: 2023-04-02T22:01:10Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-11-28T09:22:25Z day: '01' ddc: - '530' department: - _id: ScWa doi: 10.1103/PhysRevE.107.034901 ec_funded: 1 external_id: isi: - '000992142700001' file: - access_level: open_access checksum: 48f5dfe4e5f1c46c3c86805cd8f84bea content_type: application/pdf creator: swaituka date_created: 2023-11-27T09:51:48Z date_updated: 2023-11-27T09:51:48Z file_id: '14612' file_name: PhysRevE.107.034901 (1).pdf file_size: 1428631 relation: main_file success: 1 file_date_updated: 2023-11-27T09:51:48Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Accurate determination of the shapes of granular charge distributions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 107 year: '2023' ... --- _id: '13238' abstract: - lang: eng text: "We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n." acknowledgement: We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful discussions about different variants of the problem. This work is supported by the European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025, the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant 470029389 (FlexNets), 2021–2024. alternative_title: - LNCS article_processing_charge: No author: - first_name: Stefan full_name: Schmid, Stefan last_name: Schmid - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: ama: 'Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023: Structural Information and Communication Complexity . Vol 13892. Springer Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26' apa: 'Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In SIROCCO 2023: Structural Information and Communication Complexity (Vol. 13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26' chicago: 'Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” In SIROCCO 2023: Structural Information and Communication Complexity , 13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26.' ieee: 'S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation,” in SIROCCO 2023: Structural Information and Communication Complexity , Alcala de Henares, Spain, 2023, vol. 13892, pp. 576–594.' ista: 'Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023: Structural Information and Communication Complexity . SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 576–594.' mla: 'Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94, doi:10.1007/978-3-031-32733-9_26.' short: 'S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information and Communication Complexity , Springer Nature, 2023, pp. 576–594.' conference: end_date: 2023-06-09 location: Alcala de Henares, Spain name: 'SIROCCO: Structural Information and Communication Complexity' start_date: 2023-06-06 date_created: 2023-07-16T22:01:12Z date_published: 2023-05-25T00:00:00Z date_updated: 2023-11-30T10:54:51Z day: '25' department: - _id: KrPi - _id: KrCh doi: 10.1007/978-3-031-32733-9_26 ec_funded: 1 external_id: arxiv: - '2204.13459' intvolume: ' 13892' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2204.13459 month: '05' oa: 1 oa_version: Preprint page: 576-594 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: 'SIROCCO 2023: Structural Information and Communication Complexity ' publication_identifier: eissn: - 1611-3349 isbn: - '9783031327322' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14506' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13892 year: '2023' ... --- _id: '14506' abstract: - lang: eng text: "Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: ama: Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506 apa: Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506 chicago: Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506. ieee: M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023. ista: Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. mla: Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506. short: M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023. date_created: 2023-11-10T08:10:43Z date_published: 2023-11-10T00:00:00Z date_updated: 2023-11-30T10:54:51Z day: '10' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: KrPi doi: 10.15479/14506 ec_funded: 1 file: - access_level: closed checksum: 521c72818d720a52b377207b2ee87b6a content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-11-23T10:29:55Z date_updated: 2023-11-23T10:29:55Z file_id: '14598' file_name: thesis_yeo.zip file_size: 3037720 relation: source_file - access_level: open_access checksum: 0ed5d16899687aecf13d843c9878c9f2 content_type: application/pdf creator: cchlebak date_created: 2023-11-23T10:30:08Z date_updated: 2023-11-23T10:30:08Z file_id: '14599' file_name: thesis_yeo.pdf file_size: 2717256 relation: main_file success: 1 file_date_updated: 2023-11-23T10:30:08Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '162' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9969' relation: part_of_dissertation status: public - id: '13238' relation: part_of_dissertation status: public - id: '14490' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: Advances in efficiency and privacy in payment channel network analysis type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14490' abstract: - lang: eng text: Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium. acknowledgement: The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant 2020388). It was also partially supported by NCN Grant 2019/35/B/ST6/04138 and ERC Grant 885666. article_processing_charge: No author: - first_name: Zeta full_name: Avarikioti, Zeta last_name: Avarikioti - first_name: Tomasz full_name: Lizurej, Tomasz last_name: Lizurej - first_name: Tomasz full_name: Michalak, Tomasz last_name: Michalak - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: ama: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In: 43rd International Conference on Distributed Computing Systems. Vol 2023. IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037' apa: 'Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning creation games. In 43rd International Conference on Distributed Computing Systems (Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037' chicago: Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo. “Lightning Creation Games.” In 43rd International Conference on Distributed Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037. ieee: Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation games,” in 43rd International Conference on Distributed Computing Systems, Hong Kong, China, 2023, vol. 2023, pp. 603–613. ista: 'Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games. 43rd International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems vol. 2023, 603–613.' mla: Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13, doi:10.1109/ICDCS57875.2023.00037. short: Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613. conference: end_date: 2023-07-21 location: Hong Kong, China name: 'ICDCS: International Conference on Distributed Computing Systems' start_date: 2023-07-18 date_created: 2023-11-05T23:00:54Z date_published: 2023-10-11T00:00:00Z date_updated: 2023-11-30T10:54:51Z day: '11' department: - _id: KrPi doi: 10.1109/ICDCS57875.2023.00037 external_id: arxiv: - '2306.16006' intvolume: ' 2023' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.16006 month: '10' oa: 1 oa_version: Preprint page: 603-613 publication: 43rd International Conference on Distributed Computing Systems publication_identifier: eissn: - 2575-8411 isbn: - '9798350339864' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '14506' relation: dissertation_contains status: public scopus_import: '1' status: public title: Lightning creation games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '14530' abstract: - lang: eng text: 'Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. ' acknowledged_ssus: - _id: M-Shop - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 citation: ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530 apa: Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530 chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530. ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023. ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria. mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530. short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023. date_created: 2023-11-15T09:59:03Z date_published: 2023-11-16T00:00:00Z date_updated: 2023-11-30T10:55:13Z day: '16' ddc: - '530' - '570' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/14530 file: - access_level: open_access checksum: 52e1d0ab6c1abe59c82dfe8c9ff5f83a content_type: application/pdf creator: mriedl date_created: 2023-11-15T09:52:54Z date_updated: 2023-11-15T09:52:54Z file_id: '14536' file_name: Thesis_Riedl_2023_corr.pdf file_size: 36743942 relation: main_file success: 1 file_date_updated: 2023-11-15T09:52:54Z has_accepted_license: '1' keyword: - Synchronization - Collective Movement - Active Matter - Cell Migration - Active Colloids language: - iso: eng month: '11' oa: 1 oa_version: Updated Version page: '260' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10703' relation: part_of_dissertation status: public - id: '10791' relation: part_of_dissertation status: public - id: '7932' relation: part_of_dissertation status: public - id: '461' relation: part_of_dissertation status: public - id: '12726' relation: old_edition status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Synchronization in collectively moving active matter type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14547' abstract: - lang: eng text: "Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier." acknowledged_ssus: - _id: NanoFab - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan citation: ama: Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547 apa: Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547 chicago: Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547. ieee: D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023. ista: Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. mla: Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547. short: D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023. date_created: 2023-11-17T13:45:26Z date_published: 2023-11-16T00:00:00Z date_updated: 2023-11-30T10:56:04Z day: '16' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/14547 file: - access_level: open_access checksum: db0c37d213bc002125bd59690e9db246 content_type: application/pdf creator: pduc date_created: 2023-11-17T13:36:44Z date_updated: 2023-11-22T09:46:06Z file_id: '14548' file_name: Phan_Thesis_pdfa.pdf file_size: 34828019 relation: main_file - access_level: closed checksum: 8d3bd6afa279a0078ffd13e06bb6d56d content_type: application/zip creator: pduc date_created: 2023-11-17T13:44:53Z date_updated: 2023-11-17T13:47:54Z file_id: '14549' file_name: dissertation_src.zip file_size: 279319709 relation: source_file file_date_updated: 2023-11-22T09:46:06Z has_accepted_license: '1' keyword: - superconductor-semiconductor - superconductivity - Al - InAs - p-wave - superconductivity - JPA - microwave language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '80' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10851' relation: part_of_dissertation status: public - id: '13264' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: Resonant microwave spectroscopy of Al-InAs tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13264' abstract: - lang: eng text: "We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n" acknowledged_ssus: - _id: NanoFab - _id: M-Shop acknowledgement: We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303. article_number: '064032' article_processing_charge: No article_type: original author: - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan - first_name: Paul full_name: Falthansl-Scheinecker, Paul id: 85b43b21-15b2-11ec-abd3-e2c252cc2285 last_name: Falthansl-Scheinecker - first_name: Umang full_name: Mishra, Umang id: 4328fa4c-f128-11eb-9611-c107b0fe4d51 last_name: Mishra - first_name: W. M. full_name: Strickland, W. M. last_name: Strickland - first_name: D. full_name: Langone, D. last_name: Langone - first_name: J. full_name: Shabani, J. last_name: Shabani - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032 apa: Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.19.064032 chicago: Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.19.064032. ieee: D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical Society, 2023. ista: Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032. mla: Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:10.1103/PhysRevApplied.19.064032. short: D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023). date_created: 2023-07-23T22:01:12Z date_published: 2023-06-09T00:00:00Z date_updated: 2023-11-30T10:56:03Z day: '09' department: - _id: AnHi - _id: OnHo doi: 10.1103/PhysRevApplied.19.064032 external_id: arxiv: - '2206.05746' isi: - '001012022600004' intvolume: ' 19' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2206.05746 month: '06' oa: 1 oa_version: Preprint publication: Physical Review Applied publication_identifier: eissn: - 2331-7019 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '14547' relation: dissertation_contains status: public scopus_import: '1' status: public title: Gate-tunable superconductor-semiconductor parametric amplifier type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2023' ... --- _id: '14591' abstract: - lang: eng text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: Bio article_processing_charge: No author: - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Marie-Kristin full_name: Nagel, Marie-Kristin last_name: Nagel - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Annamaria full_name: Hlavata, Annamaria id: 36062FEC-F248-11E8-B48F-1D18A9856A87 last_name: Hlavata - first_name: Erika full_name: Isono, Erika last_name: Isono - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523 apa: Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523 chicago: Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523. ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. . ista: Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523. mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523. short: N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.). date_created: 2023-11-22T10:17:49Z date_published: 2023-10-10T00:00:00Z date_updated: 2023-12-01T13:51:06Z day: '10' department: - _id: JiFr - _id: MaLo - _id: CaBe doi: 10.1101/2023.10.09.561523 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2 month: '10' oa: 1 oa_version: Preprint project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: bioRxiv publication_status: submitted related_material: record: - id: '14510' relation: dissertation_contains status: public status: public title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14639' abstract: - lang: eng text: "Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”." article_number: '102' article_processing_charge: Yes article_type: original author: - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Barbara full_name: Vona, Barbara last_name: Vona - first_name: Tracy full_name: Lau, Tracy last_name: Lau - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Maha S. full_name: Zaki, Maha S. last_name: Zaki - first_name: Huda Shujaa full_name: Aldeen, Huda Shujaa last_name: Aldeen - first_name: Ehsan Ghayoor full_name: Karimiani, Ehsan Ghayoor last_name: Karimiani - first_name: Clarissa full_name: Rocca, Clarissa last_name: Rocca - first_name: Mahmoud M. full_name: Noureldeen, Mahmoud M. last_name: Noureldeen - first_name: Ahmed K. full_name: Saad, Ahmed K. last_name: Saad - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Tobias full_name: Bartolomaeus, Tobias last_name: Bartolomaeus - first_name: Rami full_name: Abou Jamra, Rami last_name: Abou Jamra - first_name: Giovanni full_name: Zifarelli, Giovanni last_name: Zifarelli - first_name: Aditi full_name: Gotkhindikar, Aditi last_name: Gotkhindikar - first_name: Ingrid M. full_name: Wentzensen, Ingrid M. last_name: Wentzensen - first_name: Mingjuan full_name: Liao, Mingjuan last_name: Liao - first_name: Emalyn Elise full_name: Cork, Emalyn Elise last_name: Cork - first_name: Pratishtha full_name: Varshney, Pratishtha last_name: Varshney - first_name: Narges full_name: Hashemi, Narges last_name: Hashemi - first_name: Mohammad Hasan full_name: Mohammadi, Mohammad Hasan last_name: Mohammadi - first_name: Aboulfazl full_name: Rad, Aboulfazl last_name: Rad - first_name: Juanita full_name: Neira, Juanita last_name: Neira - first_name: Mehran Beiraghi full_name: Toosi, Mehran Beiraghi last_name: Toosi - first_name: Cordula full_name: Knopp, Cordula last_name: Knopp - first_name: Ingo full_name: Kurth, Ingo last_name: Kurth - first_name: Thomas D. full_name: Challman, Thomas D. last_name: Challman - first_name: Rebecca full_name: Smith, Rebecca last_name: Smith - first_name: Asmahan full_name: Abdalla, Asmahan last_name: Abdalla - first_name: Thomas full_name: Haaf, Thomas last_name: Haaf - first_name: Mohnish full_name: Suri, Mohnish last_name: Suri - first_name: Manali full_name: Joshi, Manali last_name: Joshi - first_name: Wendy K. full_name: Chung, Wendy K. last_name: Chung - first_name: Andres full_name: Moreno-De-Luca, Andres last_name: Moreno-De-Luca - first_name: Henry full_name: Houlden, Henry last_name: Houlden - first_name: Reza full_name: Maroofian, Reza last_name: Maroofian - first_name: Gaurav K. full_name: Varshney, Gaurav K. last_name: Varshney citation: ama: Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01258-4 apa: Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney, G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01258-4 chicago: Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01258-4. ieee: S.-J. Lin et al., “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” Genome Medicine, vol. 15. Springer Nature, 2023. ista: Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102. mla: Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome Medicine, vol. 15, 102, Springer Nature, 2023, doi:10.1186/s13073-023-01258-4. short: S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani, C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra, G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney, N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth, T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A. Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023). date_created: 2023-12-04T08:10:55Z date_published: 2023-11-23T00:00:00Z date_updated: 2023-12-04T08:17:22Z day: '23' ddc: - '570' doi: 10.1186/s13073-023-01258-4 extern: '1' file: - access_level: open_access checksum: 279efd212005549aba817a487d56d363 content_type: application/pdf creator: dernst date_created: 2023-12-04T08:15:43Z date_updated: 2023-12-04T08:15:43Z file_id: '14640' file_name: 2023_GenomeMed_Lin.pdf file_size: 14791081 relation: main_file success: 1 file_date_updated: 2023-12-04T08:15:43Z has_accepted_license: '1' intvolume: ' 15' keyword: - Genetics (clinical) - Genetics - Molecular Biology - Molecular Medicine language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Genome Medicine publication_identifier: issn: - 1756-994X publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14628' abstract: - lang: eng text: We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration. acknowledgement: "The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program." article_number: '168' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Liane full_name: Makatura, Liane last_name: Makatura - first_name: Bohan full_name: Wang, Bohan last_name: Wang - first_name: Yi-Lu full_name: Chen, Yi-Lu id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70 last_name: Chen - first_name: Bolei full_name: Deng, Bolei last_name: Deng - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik citation: ama: 'Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3605389' apa: 'Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., & Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3605389' chicago: 'Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3605389.' ieee: 'L. Makatura et al., “Procedural metamaterials: A unified procedural graph for metamaterial design,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.' ista: 'Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.' mla: 'Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:10.1145/3605389.' short: L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023). date_created: 2023-11-29T15:02:03Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-12-04T08:09:05Z day: '01' ddc: - '531' - '006' department: - _id: GradSch - _id: ChWo - _id: BeBi doi: 10.1145/3605389 file: - access_level: open_access checksum: 0192f597d7a2ceaf89baddfd6190d4c8 content_type: application/zip creator: yichen date_created: 2023-11-29T15:16:01Z date_updated: 2023-11-29T15:16:01Z file_id: '14630' file_name: tog-22-0089-File004.zip file_size: 95467870 relation: main_file success: 1 - access_level: open_access checksum: 7fb024963be81933494f38de191e4710 content_type: application/zip creator: yichen date_created: 2023-11-29T15:16:01Z date_updated: 2023-11-29T15:16:01Z file_id: '14631' file_name: tog-22-0089-File005.zip file_size: 103731880 relation: main_file success: 1 - access_level: open_access checksum: b7d6829ce396e21cac9fae0ec7130a6b content_type: application/pdf creator: dernst date_created: 2023-12-04T08:04:14Z date_updated: 2023-12-04T08:04:14Z file_id: '14638' file_name: 2023_ACMToG_Makatura.pdf file_size: 57067476 relation: main_file success: 1 file_date_updated: 2023-12-04T08:04:14Z has_accepted_license: '1' intvolume: ' 42' issue: '5' keyword: - Computer Graphics and Computer-Aided Design language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 - 1557-7368 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: 'Procedural metamaterials: A unified procedural graph for metamaterial design' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '14644' abstract: - lang: eng text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression. acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: PreCl acknowledgement: "We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF)." article_processing_charge: No author: - first_name: Katarina full_name: Tluckova, Katarina id: 4AC7D980-F248-11E8-B48F-1D18A9856A87 last_name: Tluckova - first_name: Anita P full_name: Testa Salmazo, Anita P id: 41F1F098-F248-11E8-B48F-1D18A9856A87 last_name: Testa Salmazo - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 citation: ama: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644 apa: Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644 chicago: Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644. ieee: K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria. ista: Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644. mla: Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644. short: K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.). date_created: 2023-12-04T14:51:00Z date_published: 2023-12-05T00:00:00Z date_updated: 2023-12-05T10:37:28Z day: '05' ddc: - '572' department: - _id: CaBe doi: 10.15479/AT:ISTA:14644 file: - access_level: open_access checksum: c45608cb97ee36d7b50ba518db8e07b0 content_type: application/pdf creator: dernst date_created: 2023-12-05T10:37:02Z date_updated: 2023-12-05T10:37:02Z file_id: '14646' file_name: 2023_Tluckova_etal_REx.pdf file_size: 4892920 relation: main_file success: 1 file_date_updated: 2023-12-05T10:37:02Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version project: - _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30 grant_number: P34185 name: Regulation of mammalian transcription by noncoding RNA publication_status: submitted publisher: Institute of Science and Technology Austria status: public title: Mechanism of mammalian transcriptional repression by noncoding RNA tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14658' abstract: - lang: eng text: "We investigate spin-charge separation of a spin-\r\n1\r\n2\r\n Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom." acknowledgement: This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG)-EXC 2056-Project ID No. 390715994. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. article_number: '043039' article_processing_charge: Yes article_type: original author: - first_name: J. M. full_name: Becker, J. M. last_name: Becker - first_name: Georgios full_name: Koutentakis, Georgios id: d7b23d3a-9e21-11ec-b482-f76739596b95 last_name: Koutentakis - first_name: P. full_name: Schmelcher, P. last_name: Schmelcher citation: ama: Becker JM, Koutentakis G, Schmelcher P. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 2023;5(4). doi:10.1103/PhysRevResearch.5.043039 apa: Becker, J. M., Koutentakis, G., & Schmelcher, P. (2023). Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043039 chicago: Becker, J. M., Georgios Koutentakis, and P. Schmelcher. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043039. ieee: J. M. Becker, G. Koutentakis, and P. Schmelcher, “Spin-charge correlations in finite one-dimensional multiband Fermi systems,” Physical Review Research, vol. 5, no. 4. American Physical Society, 2023. ista: Becker JM, Koutentakis G, Schmelcher P. 2023. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 5(4), 043039. mla: Becker, J. M., et al. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research, vol. 5, no. 4, 043039, American Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043039. short: J.M. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 5 (2023). date_created: 2023-12-10T23:00:58Z date_published: 2023-10-12T00:00:00Z date_updated: 2023-12-11T10:55:52Z day: '12' ddc: - '530' department: - _id: MiLe doi: 10.1103/PhysRevResearch.5.043039 ec_funded: 1 external_id: arxiv: - '2305.09529' file: - access_level: open_access checksum: ee31c0d0de5d1b65591990ae6705a601 content_type: application/pdf creator: dernst date_created: 2023-12-11T10:49:07Z date_updated: 2023-12-11T10:49:07Z file_id: '14672' file_name: 2023_PhysReviewResearch_Becker.pdf file_size: 2362158 relation: main_file success: 1 file_date_updated: 2023-12-11T10:49:07Z has_accepted_license: '1' intvolume: ' 5' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Physical Review Research publication_identifier: issn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Spin-charge correlations in finite one-dimensional multiband Fermi systems tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2023' ... --- _id: '14650' abstract: - lang: eng text: We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures. acknowledgement: "We thank Lauriane Chomaz for useful discussions and comments on the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No. M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948 (the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967 and FOR2247." article_number: '232' article_processing_charge: No article_type: original author: - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Luis full_name: Santos, Luis last_name: Santos - first_name: Luisllu A. full_name: Peña Ardila, Luisllu A. last_name: Peña Ardila citation: ama: Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 2023;15(6). doi:10.21468/scipostphys.15.6.232 apa: Volosniev, A., Bighin, G., Santos, L., & Peña Ardila, L. A. (2023). Non-equilibrium dynamics of dipolar polarons. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.6.232 chicago: Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.6.232. ieee: A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium dynamics of dipolar polarons,” SciPost Physics, vol. 15, no. 6. SciPost Foundation, 2023. ista: Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 15(6), 232. mla: Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.6.232. short: A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15 (2023). date_created: 2023-12-10T13:03:07Z date_published: 2023-12-07T00:00:00Z date_updated: 2023-12-11T07:44:08Z day: '07' ddc: - '530' department: - _id: MiLe doi: 10.21468/scipostphys.15.6.232 ec_funded: 1 external_id: arxiv: - '2305.17969' file: - access_level: open_access checksum: e664372a1fe9d628a9bb1d135ebab7d8 content_type: application/pdf creator: dernst date_created: 2023-12-11T07:42:04Z date_updated: 2023-12-11T07:42:04Z file_id: '14669' file_name: 2023_SciPostPhysics_Volosniev.pdf file_size: 3543541 relation: main_file success: 1 file_date_updated: 2023-12-11T07:42:04Z has_accepted_license: '1' intvolume: ' 15' issue: '6' keyword: - General Physics and Astronomy language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: SciPost Physics publication_identifier: issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' status: public title: Non-equilibrium dynamics of dipolar polarons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14653' abstract: - lang: eng text: 'Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen''s motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.' acknowledgement: We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF). article_number: '117168' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Florian full_name: Kluibenschedl, Florian id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9 last_name: Kluibenschedl - first_name: Anna full_name: Ploner, Anna last_name: Ploner - first_name: Christina full_name: Meisenbichler, Christina last_name: Meisenbichler - first_name: Robert full_name: Konrat, Robert last_name: Konrat - first_name: Thomas full_name: Müller, Thomas last_name: Müller citation: ama: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 2023;495. doi:10.1016/j.ijms.2023.117168 apa: Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller, T. (2023). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168 chicago: Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier, 2023. https://doi.org/10.1016/j.ijms.2023.117168. ieee: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” International Journal of Mass Spectrometry, vol. 495. Elsevier, 2023. ista: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168. mla: Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry, vol. 495, 117168, Elsevier, 2023, doi:10.1016/j.ijms.2023.117168. short: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2023). date_created: 2023-12-10T23:00:57Z date_published: 2023-11-23T00:00:00Z date_updated: 2023-12-11T08:16:35Z day: '23' department: - _id: GradSch doi: 10.1016/j.ijms.2023.117168 intvolume: ' 495' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.ijms.2023.117168 month: '11' oa: 1 oa_version: Published Version publication: International Journal of Mass Spectrometry publication_identifier: issn: - 1387-3806 publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Advanced motion tracking for interactive mass spectrometry imaging (IMSI) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 495 year: '2023' ... --- _id: '14647' abstract: - lang: eng text: In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that new born neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex. acknowledgement: "We thank Dr. Shital Suryavanshi and the animal house staff of the Tata Institute of\r\nFundamental Research (TIFR) for their excellent support; Gord Fishell and Goichi Miyoshi for\r\nthe Foxg1 floxed mouse line; Hiroshi Kawasaki for the plasmids pCAG-FGF8 and pCAGsFGFR3c. We thank Prof. S.K. Lee for the Foxg1lox/lox genotyping primers and protocol. We thank Dr. Deepak Modi and Dr. Vainav Patel for allowing us to use the NIRRCH FACS Facility and the staff of the NIRRCH and TIFR FACS facilities for their assistance.\r\nWe thank Denis Jabaudon for his critical comments on the manuscript and members of the\r\nJabaudon lab for helpful discussions. This work was funded by the Department of Atomic\r\nEnergy (DAE), Govt. of India (Project Identification no. RTI4003, DAE OM no.\r\n1303/2/2019/R&D-II/DAE/2079)." article_processing_charge: No author: - first_name: Mahima full_name: Bose, Mahima last_name: Bose - first_name: Varun full_name: Suresh, Varun last_name: Suresh - first_name: Urvi full_name: Mishra, Urvi last_name: Mishra - first_name: Ishita full_name: Talwar, Ishita last_name: Talwar - first_name: Anuradha full_name: Yadav, Anuradha last_name: Yadav - first_name: Shiona full_name: Biswas, Shiona last_name: Biswas - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Shubha full_name: Tole, Shubha last_name: Tole citation: ama: Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv. doi:10.1101/2023.11.30.569337 apa: Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole, S. (n.d.). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.11.30.569337 chicago: Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav, Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2023.11.30.569337. ieee: M. Bose et al., “Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway,” bioRxiv. Cold Spring Harbor Laboratory. ista: Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole S. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv, 10.1101/2023.11.30.569337. mla: Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2023.11.30.569337. short: M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, BioRxiv (n.d.). date_created: 2023-12-06T13:07:01Z date_published: 2023-12-01T00:00:00Z date_updated: 2023-12-11T07:37:17Z day: '01' department: - _id: SiHi doi: 10.1101/2023.11.30.569337 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.11.30.569337 month: '12' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory status: public title: Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14655' abstract: - lang: eng text: The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division. acknowledgement: The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066). article_number: '228401' article_processing_charge: No article_type: original author: - first_name: Valerio full_name: Sorichetti, Valerio id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b last_name: Sorichetti orcid: 0000-0002-9645-6576 - first_name: Martin full_name: Lenz, Martin last_name: Lenz citation: ama: Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 2023;131(22). doi:10.1103/PhysRevLett.131.228401 apa: Sorichetti, V., & Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.228401 chicago: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.228401. ieee: V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” Physical Review Letters, vol. 131, no. 22. American Physical Society, 2023. ista: Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401. mla: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.228401. short: V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023). date_created: 2023-12-10T23:00:57Z date_published: 2023-12-01T00:00:00Z date_updated: 2023-12-11T07:59:25Z day: '01' department: - _id: AnSa doi: 10.1103/PhysRevLett.131.228401 external_id: arxiv: - '2303.03088' intvolume: ' 131' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2303.03088 month: '12' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Transverse fluctuations control the assembly of semiflexible filaments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2023' ... --- _id: '14660' abstract: - lang: eng text: "The classical Steinitz theorem states that if the origin belongs to the interior of the convex hull of a set \U0001D446⊂ℝ\U0001D451, then there are at most 2\U0001D451 points of \U0001D446 whose convex hull contains the origin in the interior. Bárány, Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem. Let \U0001D444 be a convex polytope in ℝ\U0001D451 containing the standard Euclidean unit ball \U0001D401\U0001D451. Then there exist at most 2\U0001D451 vertices of \U0001D444 whose convex hull \U0001D444′ satisfies \U0001D45F\U0001D401\U0001D451⊂\U0001D444′ with \U0001D45F⩾\U0001D451−2\U0001D451. They conjectured that \U0001D45F⩾\U0001D450\U0001D451−1∕2 holds with a universal constant \U0001D450>0. We prove \U0001D45F⩾15\U0001D4512, the first polynomial lower bound on \U0001D45F. Furthermore, we show that \U0001D45F is not greater than 2/√\U0001D451." acknowledgement: M.N. was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences aswell as the National Research, Development and Innovation Fund (NRDI) grants K119670 andK131529, and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovationand Technology from the source of the NRDI as well as the ELTE TKP 2021-NKTA-62 fundingscheme article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Márton full_name: Naszódi, Márton last_name: Naszódi citation: ama: 'Ivanov G, Naszódi M. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. 2023. doi:10.1112/blms.12965' apa: 'Ivanov, G., & Naszódi, M. (2023). Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12965' chicago: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society. London Mathematical Society, 2023. https://doi.org/10.1112/blms.12965.' ieee: 'G. Ivanov and M. Naszódi, “Quantitative Steinitz theorem: A polynomial bound,” Bulletin of the London Mathematical Society. London Mathematical Society, 2023.' ista: 'Ivanov G, Naszódi M. 2023. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society.' mla: 'Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society, London Mathematical Society, 2023, doi:10.1112/blms.12965.' short: G. Ivanov, M. Naszódi, Bulletin of the London Mathematical Society (2023). date_created: 2023-12-10T23:00:58Z date_published: 2023-12-04T00:00:00Z date_updated: 2023-12-11T10:03:54Z day: '04' department: - _id: UlWa doi: 10.1112/blms.12965 external_id: arxiv: - '2212.04308' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1112/blms.12965' month: '12' oa: 1 oa_version: Published Version publication: Bulletin of the London Mathematical Society publication_identifier: eissn: - 1469-2120 issn: - 0024-6093 publication_status: epub_ahead publisher: London Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Quantitative Steinitz theorem: A polynomial bound' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14666' abstract: - lang: eng text: So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function. acknowledgement: We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott, A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson, B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback. This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council grant (UKRI-BBSRC BB/N019512/1). article_number: e2306525120 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Chaitanya full_name: Chintaluri, Chaitanya id: E4EDB536-3485-11EA-98D2-20AF3DDC885E last_name: Chintaluri - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(48). doi:10.1073/pnas.2306525120 apa: Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120 chicago: Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120. ieee: C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48. National Academy of Sciences, 2023. ista: Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 120(48), e2306525120. mla: Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120. short: C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023). date_created: 2023-12-10T23:01:00Z date_published: 2023-11-21T00:00:00Z date_updated: 2023-12-11T12:47:41Z day: '21' ddc: - '570' department: - _id: TiVo doi: 10.1073/pnas.2306525120 external_id: pmid: - '37988463' file: - access_level: open_access checksum: bf4ec38602a70dae4338077a5a4d497f content_type: application/pdf creator: dernst date_created: 2023-12-11T12:45:12Z date_updated: 2023-12-11T12:45:12Z file_id: '14678' file_name: 2023_PNAS_Chintaluri.pdf file_size: 16891602 relation: main_file success: 1 file_date_updated: 2023-12-11T12:45:12Z has_accepted_license: '1' intvolume: ' 120' issue: '48' language: - iso: eng month: '11' oa: 1 oa_version: None pmid: 1 project: - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ccluri/metabolic_spiking scopus_import: '1' status: public title: Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 120 year: '2023' ... --- _id: '14656' abstract: - lang: eng text: Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain. acknowledgement: M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Michele full_name: Nardin, Michele id: 30BD0376-F248-11E8-B48F-1D18A9856A87 last_name: Nardin orcid: 0000-0001-8849-6570 - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin citation: ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023 apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023 chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023. ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023. ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156. mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023. short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156. date_created: 2023-12-10T23:00:58Z date_published: 2023-11-29T00:00:00Z date_updated: 2023-12-11T11:37:20Z day: '29' ddc: - '570' department: - _id: JoCs - _id: GaTk doi: 10.1523/JNEUROSCI.0194-23.2023 ec_funded: 1 external_id: pmid: - '37758476' file: - access_level: closed checksum: e2503c8f84be1050e28f64320f1d5bd2 content_type: application/pdf creator: dernst date_created: 2023-12-11T11:30:37Z date_updated: 2023-12-11T11:30:37Z embargo: 2024-06-01 embargo_to: open_access file_id: '14674' file_name: 2023_JourNeuroscience_Nardin.pdf file_size: 2280632 relation: main_file file_date_updated: 2023-12-11T11:30:37Z has_accepted_license: '1' intvolume: ' 43' issue: '48' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1523/JNEUROSCI.0194-23.2023 month: '11' oa: 1 oa_version: Published Version page: 8140-8156 pmid: 1 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: The Journal of Neuroscience publication_identifier: eissn: - 1529-2401 publication_status: published publisher: Society of Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: The structure of hippocampal CA1 interactions optimizes spatial coding across experience tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2023' ... --- _id: '14657' abstract: - lang: eng text: 'Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.' acknowledgement: K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004). article_number: '20230355' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Kamran full_name: Kaveh, Kamran last_name: Kaveh - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 2023;20(208). doi:10.1098/rsif.2023.0355 apa: Tkadlec, J., Kaveh, K., Chatterjee, K., & Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. The Royal Society. https://doi.org/10.1098/rsif.2023.0355 chicago: Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society, Interface. The Royal Society, 2023. https://doi.org/10.1098/rsif.2023.0355. ieee: J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” Journal of the Royal Society, Interface, vol. 20, no. 208. The Royal Society, 2023. ista: Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 20(208), 20230355. mla: Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society, Interface, vol. 20, no. 208, 20230355, The Royal Society, 2023, doi:10.1098/rsif.2023.0355. short: J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society, Interface 20 (2023). date_created: 2023-12-10T23:00:58Z date_published: 2023-11-29T00:00:00Z date_updated: 2023-12-11T11:17:53Z day: '29' ddc: - '000' - '570' department: - _id: KrCh doi: 10.1098/rsif.2023.0355 ec_funded: 1 external_id: pmid: - '38016637' file: - access_level: open_access checksum: 2eefab13127c7786dbd33303c482a004 content_type: application/pdf creator: dernst date_created: 2023-12-11T11:10:32Z date_updated: 2023-12-11T11:10:32Z file_id: '14673' file_name: 2023_RoyalInterface_Tkadlec.pdf file_size: 1720243 relation: main_file success: 1 file_date_updated: 2023-12-11T11:10:32Z has_accepted_license: '1' intvolume: ' 20' issue: '208' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: Journal of the Royal Society, Interface publication_identifier: eissn: - 1742-5662 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: Evolutionary dynamics of mutants that modify population structure tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2023' ... --- _id: '14664' abstract: - lang: eng text: The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts “on demand”. acknowledgement: We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program under the European Research Council (grant agreement 820008).We also thank the Deutsche Forschungsgemeinschaft (DFG) for support through priority program SPP1807(CL489/3-2) and RESOLV Cluster of Excellence EXC2033 (project number 390677874). A.B.G. acknowledges funding from the Zuckerman STEM Leadership Program. DFT calculations were carried out using resources provided by the Wrocław Center for Networking and Supercomputing, grant 329. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Kuntrapakam full_name: Hema, Kuntrapakam last_name: Hema - first_name: Angela B. full_name: Grommet, Angela B. last_name: Grommet - first_name: Michał J. full_name: Białek, Michał J. last_name: Białek - first_name: Jinhua full_name: Wang, Jinhua last_name: Wang - first_name: Laura full_name: Schneider, Laura last_name: Schneider - first_name: Christoph full_name: Drechsler, Christoph last_name: Drechsler - first_name: Oksana full_name: Yanshyna, Oksana last_name: Yanshyna - first_name: Yael full_name: Diskin-Posner, Yael last_name: Diskin-Posner - first_name: Guido H. full_name: Clever, Guido H. last_name: Clever - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Hema K, Grommet AB, Białek MJ, et al. Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. 2023;145(45):24755-24764. doi:10.1021/jacs.3c08666 apa: Hema, K., Grommet, A. B., Białek, M. J., Wang, J., Schneider, L., Drechsler, C., … Klajn, R. (2023). Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c08666 chicago: Hema, Kuntrapakam, Angela B. Grommet, Michał J. Białek, Jinhua Wang, Laura Schneider, Christoph Drechsler, Oksana Yanshyna, Yael Diskin-Posner, Guido H. Clever, and Rafal Klajn. “Guest Encapsulation Alters the Thermodynamic Landscape of a Coordination Host.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c08666. ieee: K. Hema et al., “Guest encapsulation alters the thermodynamic landscape of a coordination host,” Journal of the American Chemical Society, vol. 145, no. 45. American Chemical Society, pp. 24755–24764, 2023. ista: Hema K, Grommet AB, Białek MJ, Wang J, Schneider L, Drechsler C, Yanshyna O, Diskin-Posner Y, Clever GH, Klajn R. 2023. Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. 145(45), 24755–24764. mla: Hema, Kuntrapakam, et al. “Guest Encapsulation Alters the Thermodynamic Landscape of a Coordination Host.” Journal of the American Chemical Society, vol. 145, no. 45, American Chemical Society, 2023, pp. 24755–64, doi:10.1021/jacs.3c08666. short: K. Hema, A.B. Grommet, M.J. Białek, J. Wang, L. Schneider, C. Drechsler, O. Yanshyna, Y. Diskin-Posner, G.H. Clever, R. Klajn, Journal of the American Chemical Society 145 (2023) 24755–24764. date_created: 2023-12-10T23:00:59Z date_published: 2023-11-02T00:00:00Z date_updated: 2023-12-11T11:47:07Z day: '02' ddc: - '540' department: - _id: RaKl doi: 10.1021/jacs.3c08666 external_id: pmid: - '37917939' file: - access_level: open_access checksum: a1f37df6b83f88f51ba64468ce0c1589 content_type: application/pdf creator: dernst date_created: 2023-12-11T11:44:54Z date_updated: 2023-12-11T11:44:54Z file_id: '14675' file_name: 2023_JACS_Hema.pdf file_size: 4304472 relation: main_file success: 1 file_date_updated: 2023-12-11T11:44:54Z has_accepted_license: '1' intvolume: ' 145' issue: '45' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 24755-24764 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Guest encapsulation alters the thermodynamic landscape of a coordination host tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2023' ...