--- _id: '12726' abstract: - lang: eng text: "Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits 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/at:ista:12726 apa: Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726 chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726. 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/at:ista:12726. short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023. date_created: 2023-03-15T13:22:13Z date_published: 2023-03-23T00:00:00Z date_updated: 2023-11-30T10:55:13Z day: '23' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:12726 file: - access_level: closed checksum: eba0e19fe57a8c15e7aeab55a845efb7 content_type: application/pdf creator: cchlebak date_created: 2023-03-23T12:49:23Z date_updated: 2023-11-24T11:57:46Z description: the main file is missing the bibliography. See new thesis record 14530 for updated files. file_id: '12745' file_name: Thesis_Riedl_2023.pdf file_size: 63734746 relation: main_file - access_level: closed checksum: 0eb7b650cc8ae843bcec7c8a6109ae03 content_type: application/octet-stream creator: cchlebak date_created: 2023-03-23T12:54:34Z date_updated: 2023-09-24T22:30:03Z embargo_to: open_access file_id: '12746' file_name: Thesis_Riedl_2023_source.rar file_size: 339473651 relation: source_file file_date_updated: 2023-11-24T11:57:46Z has_accepted_license: '1' language: - iso: eng month: '03' oa_version: None 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: '14530' relation: new_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: '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 license: https://creativecommons.org/licenses/by-nc-sa/4.0/ 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 license: https://creativecommons.org/licenses/by/4.0/ 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 license: https://creativecommons.org/licenses/by-nc/4.0/ 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' ... --- _id: '14663' abstract: - lang: eng text: As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity. acknowledgement: The authors acknowledge the financial support from the National Natural Science Foundation of China (22008211, 92045303, U21A20298), the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), and Zhejiang Innovation Team (2017R5203). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jinyan full_name: Zhao, Jinyan last_name: Zhao - first_name: Zihao full_name: Yao, Zihao last_name: Yao - first_name: Rhys full_name: Bunting, Rhys id: 91deeae8-1207-11ec-b130-c194ad5b50c6 last_name: Bunting orcid: 0000-0001-6928-074X - first_name: P. full_name: Hu, P. last_name: Hu - first_name: Jianguo full_name: Wang, Jianguo last_name: Wang citation: ama: Zhao J, Yao Z, Bunting R, Hu P, Wang J. Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. 2023;13(22):15054-15073. doi:10.1021/acscatal.3c03893 apa: Zhao, J., Yao, Z., Bunting, R., Hu, P., & Wang, J. (2023). Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. American Chemical Society. https://doi.org/10.1021/acscatal.3c03893 chicago: Zhao, Jinyan, Zihao Yao, Rhys Bunting, P. Hu, and Jianguo Wang. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis. American Chemical Society, 2023. https://doi.org/10.1021/acscatal.3c03893. ieee: J. Zhao, Z. Yao, R. Bunting, P. Hu, and J. Wang, “Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles,” ACS Catalysis, vol. 13, no. 22. American Chemical Society, pp. 15054–15073, 2023. ista: Zhao J, Yao Z, Bunting R, Hu P, Wang J. 2023. Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. 13(22), 15054–15073. mla: Zhao, Jinyan, et al. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis, vol. 13, no. 22, American Chemical Society, 2023, pp. 15054–73, doi:10.1021/acscatal.3c03893. short: J. Zhao, Z. Yao, R. Bunting, P. Hu, J. Wang, ACS Catalysis 13 (2023) 15054–15073. date_created: 2023-12-10T23:00:59Z date_published: 2023-11-06T00:00:00Z date_updated: 2023-12-11T11:55:35Z day: '06' ddc: - '540' department: - _id: MaIb doi: 10.1021/acscatal.3c03893 file: - access_level: open_access checksum: a97c771077af71ddfb2249e34530895c content_type: application/pdf creator: dernst date_created: 2023-12-11T11:55:09Z date_updated: 2023-12-11T11:55:09Z file_id: '14676' file_name: 2023_ACSCatalysis_.pdf file_size: 14813812 relation: main_file success: 1 file_date_updated: 2023-12-11T11:55:09Z has_accepted_license: '1' intvolume: ' 13' issue: '22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 15054-15073 publication: ACS Catalysis publication_identifier: eissn: - 2155-5435 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles 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: '14667' abstract: - lang: eng text: 'For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum. ' - lang: fre text: On étudie les fluctuations de f (X), où X est une matrice aléatoire non-hermitienne de grande taille à coefficients i.i.d. (réels ou complexes), et f une fonction analytique sur un domaine qui contient le spectre de X. On prouve que, pour une matrice carrée générique et bornée A, les fluctuations de la quantité tr f (X)A sont asymptotiquement gaussiennes et comportent deux modes indépendants, correspondant aux composantes traciale et de trace nulle de A. Une nouvelle formule est établie pour la variance de la composante de trace nulle, qui fait intervenir la norme de Frobenius de A et la norme L2 de f sur la frontière du spectre limite. acknowledgement: "The first author was partially supported by ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nThe authors are grateful to the anonymous referees and associated editor for carefully reading this paper and providing helpful comments that improved the quality of the article. Also the authors would like to thank Peter Forrester for pointing out the reference [12] that was absent in the previous version of the manuscript." article_processing_charge: No article_type: original author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Hong Chang full_name: Ji, Hong Chang id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d last_name: Ji citation: ama: Erdös L, Ji HC. Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2023;59(4):2083-2105. doi:10.1214/22-AIHP1304 apa: Erdös, L., & Ji, H. C. (2023). Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1304 chicago: Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AIHP1304. ieee: L. Erdös and H. C. Ji, “Functional CLT for non-Hermitian random matrices,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 59, no. 4. Institute of Mathematical Statistics, pp. 2083–2105, 2023. ista: Erdös L, Ji HC. 2023. Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 59(4), 2083–2105. mla: Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 59, no. 4, Institute of Mathematical Statistics, 2023, pp. 2083–105, doi:10.1214/22-AIHP1304. short: L. Erdös, H.C. Ji, Annales de l’institut Henri Poincare (B) Probability and Statistics 59 (2023) 2083–2105. date_created: 2023-12-10T23:01:00Z date_published: 2023-11-01T00:00:00Z date_updated: 2023-12-11T12:36:56Z day: '01' department: - _id: LaEr doi: 10.1214/22-AIHP1304 ec_funded: 1 external_id: arxiv: - '2112.11382' intvolume: ' 59' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2112.11382 month: '11' oa: 1 oa_version: Preprint page: 2083-2105 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Annales de l'institut Henri Poincare (B) Probability and Statistics publication_identifier: issn: - 0246-0203 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Functional CLT for non-Hermitian random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 59 year: '2023' ... --- _id: '14662' abstract: - lang: eng text: "We consider a class of polaron models, including the Fröhlich model, at zero total\r\nmomentum, and show that at sufficiently weak coupling there are no excited eigenvalues below\r\nthe essential spectrum." article_processing_charge: Yes article_type: original author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. 2023;13(3):1045-1055. doi:10.4171/JST/469 apa: Seiringer, R. (2023). Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/469 chicago: Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/469. ieee: R. Seiringer, “Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling,” Journal of Spectral Theory, vol. 13, no. 3. EMS Press, pp. 1045–1055, 2023. ista: Seiringer R. 2023. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. 13(3), 1045–1055. mla: Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” Journal of Spectral Theory, vol. 13, no. 3, EMS Press, 2023, pp. 1045–55, doi:10.4171/JST/469. short: R. Seiringer, Journal of Spectral Theory 13 (2023) 1045–1055. date_created: 2023-12-10T23:00:59Z date_published: 2023-11-25T00:00:00Z date_updated: 2023-12-11T12:12:14Z day: '25' ddc: - '510' department: - _id: RoSe doi: 10.4171/JST/469 external_id: arxiv: - '2210.17123' file: - access_level: open_access checksum: 9ce96ca87d56ea9a70d2eb9a32839f8d content_type: application/pdf creator: dernst date_created: 2023-12-11T12:03:12Z date_updated: 2023-12-11T12:03:12Z file_id: '14677' file_name: 2023_JST_Seiringer.pdf file_size: 201513 relation: main_file success: 1 file_date_updated: 2023-12-11T12:03:12Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '11' oa: 1 oa_version: None page: 1045-1055 publication: Journal of Spectral Theory publication_identifier: eissn: - 1664-0403 issn: - 1664-039X publication_status: published publisher: EMS Press quality_controlled: '1' scopus_import: '1' status: public title: Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling 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: '14652' abstract: - lang: eng text: In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli. article_number: '415539' article_processing_charge: No article_type: original author: - first_name: Shyam Lal full_name: Gupta, Shyam Lal last_name: Gupta - first_name: Saurabh full_name: Singh, Saurabh id: 12d625da-9cb3-11ed-9667-af09d37d3f0a last_name: Singh orcid: 0000-0003-2209-5269 - first_name: Sumit full_name: Kumar, Sumit last_name: Kumar - first_name: Unknown full_name: Anupam, Unknown last_name: Anupam - first_name: Samjeet Singh full_name: Thakur, Samjeet Singh last_name: Thakur - first_name: Ashish full_name: Kumar, Ashish last_name: Kumar - first_name: Sanjay full_name: Panwar, Sanjay last_name: Panwar - first_name: D. full_name: Diwaker, D. last_name: Diwaker citation: ama: 'Gupta SL, Singh S, Kumar S, et al. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. 2023;674. doi:10.1016/j.physb.2023.415539' apa: 'Gupta, S. L., Singh, S., Kumar, S., Anupam, U., Thakur, S. S., Kumar, A., … Diwaker, D. (2023). Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2023.415539' chicago: 'Gupta, Shyam Lal, Saurabh Singh, Sumit Kumar, Unknown Anupam, Samjeet Singh Thakur, Ashish Kumar, Sanjay Panwar, and D. Diwaker. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” Physica B: Condensed Matter. Elsevier, 2023. https://doi.org/10.1016/j.physb.2023.415539.' ieee: 'S. L. Gupta et al., “Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys,” Physica B: Condensed Matter, vol. 674. Elsevier, 2023.' ista: 'Gupta SL, Singh S, Kumar S, Anupam U, Thakur SS, Kumar A, Panwar S, Diwaker D. 2023. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. 674, 415539.' mla: 'Gupta, Shyam Lal, et al. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” Physica B: Condensed Matter, vol. 674, 415539, Elsevier, 2023, doi:10.1016/j.physb.2023.415539.' short: 'S.L. Gupta, S. Singh, S. Kumar, U. Anupam, S.S. Thakur, A. Kumar, S. Panwar, D. Diwaker, Physica B: Condensed Matter 674 (2023).' date_created: 2023-12-10T23:00:56Z date_published: 2023-11-28T00:00:00Z date_updated: 2023-12-12T08:22:23Z day: '28' department: - _id: MaIb doi: 10.1016/j.physb.2023.415539 intvolume: ' 674' language: - iso: eng month: '11' oa_version: None publication: 'Physica B: Condensed Matter' publication_identifier: issn: - 0921-4526 publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 674 year: '2023' ... --- _id: '12487' abstract: - lang: eng text: Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis. acknowledgement: FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP. article_processing_charge: Yes article_type: original author: - first_name: Silvia full_name: Scarpetta, Silvia last_name: Scarpetta - first_name: Niccolò full_name: Morrisi, Niccolò last_name: Morrisi - first_name: Carlotta full_name: Mutti, Carlotta last_name: Mutti - first_name: Nicoletta full_name: Azzi, Nicoletta last_name: Azzi - first_name: Irene full_name: Trippi, Irene last_name: Trippi - first_name: Rosario full_name: Ciliento, Rosario last_name: Ciliento - first_name: Ilenia full_name: Apicella, Ilenia last_name: Apicella - first_name: Giovanni full_name: Messuti, Giovanni last_name: Messuti - first_name: Marianna full_name: Angiolelli, Marianna last_name: Angiolelli - first_name: Fabrizio full_name: Lombardi, Fabrizio id: A057D288-3E88-11E9-986D-0CF4E5697425 last_name: Lombardi orcid: 0000-0003-2623-5249 - first_name: Liborio full_name: Parrino, Liborio last_name: Parrino - first_name: Anna Elisabetta full_name: Vaudano, Anna Elisabetta last_name: Vaudano citation: ama: Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 2023;26(10):107840. doi:10.1016/j.isci.2023.107840 apa: Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107840 chicago: Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840. ieee: S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” iScience, vol. 26, no. 10. Elsevier, p. 107840, 2023. ista: Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840. mla: Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:10.1016/j.isci.2023.107840. short: S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840. date_created: 2023-02-02T10:50:17Z date_published: 2023-10-20T00:00:00Z date_updated: 2023-12-13T11:11:24Z day: '20' ddc: - '570' department: - _id: GaTk doi: 10.1016/j.isci.2023.107840 ec_funded: 1 external_id: isi: - '001082331200001' pmid: - '37766992' file: - access_level: open_access checksum: f499836af172ecc9865de4bb41fa99d1 content_type: application/pdf creator: dernst date_created: 2023-10-09T07:23:46Z date_updated: 2023-10-09T07:23:46Z file_id: '14412' file_name: 2023_iScience_Scarpetta.pdf file_size: 4872708 relation: main_file success: 1 file_date_updated: 2023-10-09T07:23:46Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '107840' pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb943429-77a9-11ec-83b8-9f471cdf5c67 grant_number: M03318 name: Functional Advantages of Critical Brain Dynamics publication: iScience publication_identifier: eissn: - 2589-0042 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture 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: 26 year: '2023' ... --- _id: '12696' abstract: - lang: eng text: "Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force.\r\nResults: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on.\r\nConclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk." acknowledged_ssus: - _id: LifeSc acknowledgement: "We are thankful to Mike Bidochka for the fungal strain, Lukas Schrader for sharing the C. obscurior genome data for primer development, the Lab Support Facility of ISTA for general laboratory support and help with the permit approval procedures, and the Finca El Quinto for letting us collect ants on their property. We thank the Social Immunity Team at ISTA for help with ant collection and experimental help, in particular Elina Hanhimäki and Marta Gorecka for behavioural observation, and Elisabeth Naderlinger for spore load PCRs. We further thank the Social Immunity Team and Jürgen Heinze for continued discussion and comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology Austria (ISTA). This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 771402 to SC). " article_number: '37' article_processing_charge: Yes article_type: original author: - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler orcid: 0000-0002-9547-2494 - first_name: Jessica full_name: Kirchner, Jessica id: 21516227-15aa-11ec-9fb2-c6e8ffc155d3 last_name: Kirchner - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Metzler S, Kirchner J, Grasse AV, Cremer S. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 2023;23. doi:10.1186/s12862-023-02137-7 apa: Metzler, S., Kirchner, J., Grasse, A. V., & Cremer, S. (2023). Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. Springer Nature. https://doi.org/10.1186/s12862-023-02137-7 chicago: Metzler, Sina, Jessica Kirchner, Anna V Grasse, and Sylvia Cremer. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” BMC Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1186/s12862-023-02137-7. ieee: S. Metzler, J. Kirchner, A. V. Grasse, and S. Cremer, “Trade-offs between immunity and competitive ability in fighting ant males,” BMC Ecology and Evolution, vol. 23. Springer Nature, 2023. ista: Metzler S, Kirchner J, Grasse AV, Cremer S. 2023. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 23, 37. mla: Metzler, Sina, et al. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” BMC Ecology and Evolution, vol. 23, 37, Springer Nature, 2023, doi:10.1186/s12862-023-02137-7. short: S. Metzler, J. Kirchner, A.V. Grasse, S. Cremer, BMC Ecology and Evolution 23 (2023). date_created: 2023-02-28T07:38:17Z date_published: 2023-08-07T00:00:00Z date_updated: 2023-12-13T11:13:14Z day: '07' ddc: - '570' department: - _id: SyCr doi: 10.1186/s12862-023-02137-7 ec_funded: 1 external_id: isi: - '001042643600002' pmid: - '37550612' file: - access_level: open_access checksum: 95966dc7d242d2c85bdd4fe14233dbd8 content_type: application/pdf creator: dernst date_created: 2023-08-14T07:51:47Z date_updated: 2023-08-14T07:51:47Z file_id: '14048' file_name: 2023_BMCEcology_Metzler.pdf file_size: 2004276 relation: main_file success: 1 file_date_updated: 2023-08-14T07:51:47Z has_accepted_license: '1' intvolume: ' 23' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip publication: BMC Ecology and Evolution publication_identifier: issn: - 2730-7182 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '12693' relation: research_data status: public scopus_import: '1' status: public title: Trade-offs between immunity and competitive ability in fighting ant males 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: 23 year: '2023' ... --- _id: '14659' abstract: - lang: eng text: Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment. acknowledgement: This work was carried out within the framework of the EV-K2-CNR and Nepal Academy of Science and Technology. K.Y. was supported by the Second Tibetan Plateau Scientific Expedition and Research Program (grant no. 2019QZKK0206). N.C. was supported by the project NODES, which has received funding from the MUR–M4C2 1.5 of PNRR funded by the European Union - NextGeneration EU (Grant agreement no. ECS00000036). T.E.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant no. 101026058. F.P. has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant no. 772751, RAVEN, ‘Rapid mass losses of debris-covered glaciers in High Mountain Asia’ and has been supported by the SNSF grant ‘High-elevation precipitation in High Mountain Asia’ (grant no. 183633). A.A. was supported by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 101004156 (CONFESS project) and by the European Union’s Horizon Europe research and innovation program under grant agreement no. 101081193 (OptimESM project). We thank H. Wehrli for valuable comments and suggestions and J. Giannitrapani for the graphic support. We thank A. Da Polenza and K. Bista of EV-K2-CNR for believing that studying the high elevations is relevant for the whole globe. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Franco full_name: Salerno, Franco last_name: Salerno - first_name: Nicolas full_name: Guyennon, Nicolas last_name: Guyennon - first_name: Kun full_name: Yang, Kun last_name: Yang - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw orcid: 0000-0001-7640-6152 - first_name: Changgui full_name: Lin, Changgui last_name: Lin - first_name: Nicola full_name: Colombo, Nicola last_name: Colombo - first_name: Emanuele full_name: Romano, Emanuele last_name: Romano - first_name: Stephan full_name: Gruber, Stephan last_name: Gruber - first_name: Tobias full_name: Bolch, Tobias last_name: Bolch - first_name: Andrea full_name: Alessandri, Andrea last_name: Alessandri - first_name: Paolo full_name: Cristofanelli, Paolo last_name: Cristofanelli - first_name: Davide full_name: Putero, Davide last_name: Putero - first_name: Guglielmina full_name: Diolaiuti, Guglielmina last_name: Diolaiuti - first_name: Gianni full_name: Tartari, Gianni last_name: Tartari - first_name: Gianpietro full_name: Verza, Gianpietro last_name: Verza - first_name: Sudeep full_name: Thakuri, Sudeep last_name: Thakuri - first_name: Gianpaolo full_name: Balsamo, Gianpaolo last_name: Balsamo - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: Salerno F, Guyennon N, Yang K, et al. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 2023;16:1120-1127. doi:10.1038/s41561-023-01331-y apa: Salerno, F., Guyennon, N., Yang, K., Shaw, T., Lin, C., Colombo, N., … Pellicciotti, F. (2023). Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. Springer Nature. https://doi.org/10.1038/s41561-023-01331-y chicago: Salerno, Franco, Nicolas Guyennon, Kun Yang, Thomas Shaw, Changgui Lin, Nicola Colombo, Emanuele Romano, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” Nature Geoscience. Springer Nature, 2023. https://doi.org/10.1038/s41561-023-01331-y. ieee: F. Salerno et al., “Local cooling and drying induced by Himalayan glaciers under global warming,” Nature Geoscience, vol. 16. Springer Nature, pp. 1120–1127, 2023. ista: Salerno F, Guyennon N, Yang K, Shaw T, Lin C, Colombo N, Romano E, Gruber S, Bolch T, Alessandri A, Cristofanelli P, Putero D, Diolaiuti G, Tartari G, Verza G, Thakuri S, Balsamo G, Miles ES, Pellicciotti F. 2023. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 16, 1120–1127. mla: Salerno, Franco, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” Nature Geoscience, vol. 16, Springer Nature, 2023, pp. 1120–27, doi:10.1038/s41561-023-01331-y. short: F. Salerno, N. Guyennon, K. Yang, T. Shaw, C. Lin, N. Colombo, E. Romano, S. Gruber, T. Bolch, A. Alessandri, P. Cristofanelli, D. Putero, G. Diolaiuti, G. Tartari, G. Verza, S. Thakuri, G. Balsamo, E.S. Miles, F. Pellicciotti, Nature Geoscience 16 (2023) 1120–1127. date_created: 2023-12-10T23:00:58Z date_published: 2023-12-04T00:00:00Z date_updated: 2023-12-13T11:01:10Z day: '04' ddc: - '550' department: - _id: FrPe doi: 10.1038/s41561-023-01331-y file: - access_level: open_access checksum: d5ae0d17069eebc6f454c8608cf83e21 content_type: application/pdf creator: dernst date_created: 2023-12-11T10:11:19Z date_updated: 2023-12-11T10:11:19Z file_id: '14671' file_name: 2023_NatureGeoscience_Salerno.pdf file_size: 6072603 relation: main_file success: 1 file_date_updated: 2023-12-11T10:11:19Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1120-1127 publication: Nature Geoscience publication_identifier: eissn: - 1752-0908 issn: - 1752-0894 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/wind-of-climate-change/ scopus_import: '1' status: public title: Local cooling and drying induced by Himalayan glaciers under global warming 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: '12786' abstract: - lang: eng text: AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators. acknowledgement: We thank James Krieger for generating the ‘proDy’ interaction maps in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript. We thank members of the Greger lab for insightful comments during this study. We acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also grateful to LMB scientific computing and the EM facility for their support. This research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Further funding came from the Medical Research Council (MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N. article_number: '1659' article_processing_charge: No article_type: original author: - first_name: Danyang full_name: Zhang, Danyang last_name: Zhang - first_name: Remigijus full_name: Lape, Remigijus last_name: Lape - first_name: Saher A. full_name: Shaikh, Saher A. last_name: Shaikh - first_name: Bianka K. full_name: Kohegyi, Bianka K. last_name: Kohegyi - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Ondrej full_name: Cais, Ondrej last_name: Cais - first_name: Terunaga full_name: Nakagawa, Terunaga last_name: Nakagawa - first_name: Ingo H. full_name: Greger, Ingo H. last_name: Greger citation: ama: Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 2023;14. doi:10.1038/s41467-023-37259-5 apa: Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., … Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37259-5 chicago: Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37259-5. ieee: D. Zhang et al., “Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 14, 1659. mla: Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications, vol. 14, 1659, Springer Nature, 2023, doi:10.1038/s41467-023-37259-5. short: D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023). date_created: 2023-04-02T22:01:09Z date_published: 2023-03-25T00:00:00Z date_updated: 2023-12-13T11:15:58Z day: '25' ddc: - '570' department: - _id: PeJo doi: 10.1038/s41467-023-37259-5 external_id: isi: - '001066658700003' file: - access_level: open_access checksum: 0a97b31191432dae5853bbb5ccb7698d content_type: application/pdf creator: dernst date_created: 2023-04-03T06:38:56Z date_updated: 2023-04-03T06:38:56Z file_id: '12797' file_name: 2023_NatureComm_Zhang.pdf file_size: 2613996 relation: main_file success: 1 file_date_updated: 2023-04-03T06:38:56Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics 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: '12693' abstract: - lang: eng text: See Readme File for further information. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:10.15479/AT:ISTA:12693' apa: 'Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12693' chicago: 'Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12693.' ieee: 'S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.' ista: 'Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12693.' mla: 'Cremer, Sylvia. Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12693.' short: S. Cremer, (2023). contributor: - contributor_type: data_collector first_name: Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler - contributor_type: data_collector first_name: Jessica id: 21516227-15aa-11ec-9fb2-c6e8ffc155d3 last_name: Kirchner - contributor_type: data_collector first_name: Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse date_created: 2023-02-28T06:38:37Z date_published: 2023-02-28T00:00:00Z date_updated: 2023-12-13T11:13:13Z day: '28' ddc: - '570' department: - _id: SyCr doi: 10.15479/AT:ISTA:12693 file: - access_level: open_access checksum: c1565d655ca05601acfd84e0d12b8563 content_type: application/pdf creator: scremer date_created: 2023-02-28T06:34:08Z date_updated: 2023-02-28T06:34:08Z file_id: '12694' file_name: Metzler_ReadMe.pdf file_size: 77070 relation: main_file success: 1 - access_level: open_access checksum: 75c4c4948563d6261cb7548f80d909f1 content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: scremer date_created: 2023-02-28T06:34:12Z date_updated: 2023-02-28T06:34:12Z file_id: '12695' file_name: Metzler_RepositoryData.xlsx file_size: 88001 relation: main_file success: 1 file_date_updated: 2023-02-28T06:34:12Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12696' relation: used_in_publication status: public status: public title: 'Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ' 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13168' abstract: - lang: eng text: Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways. acknowledgement: This work received support from the European Union-funded Horizon Europe project ‘environMENTAL’ (no. 101057429 to G.S., A.M. and M.M.N.) and cofunding by UK Research and Innovation under the UK Government’s Horizon Europe funding guarantee (nos. 10041392 and 10038599) for study design and data analysis; the Horizon 2020-funded European Research Council Advanced Grant ‘STRATIFY’ (no. 695313 to G.S. for study design and data analysis); the Human Brain Project (HBP SGA3, no. 945539 to G.S. for study design and data analysis); the National Institutes of Health (grant no. R01DA049238 to G.S. for study design and data analysis); the German Research Foundation (COPE; grant no. 675346 to G.S. for study design and data analysis); the National Natural Science Foundation of China (grant no. 82001797 to J.X., grant no. 82030053 to C.Y., grant no. 82202093 to J.T. and grant no. 82150710554 to G.S. for study design, data analysis and preparation of the manuscript); National Key Research and Development Program of China (grant no. 2018YFC1314301 to C.Y. for study design and data analysis); Tianjin Applied Basic Research Diversified Investment Foundation (grant no. 21JCYBJC01360 to J.X. for study design and data analysis); Tianjin Health Technology Project (grant no. TJWJ2021QN002 to J.X. for preparation of the manuscript); Science & Technology Development Fund of the Tianjin Education Commission for Higher Education (grant no. 2019KJ195 to J.X. for preparation of the manuscript); the Tianjin Medical University ‘Clinical Talent Training 123 Climbing Plan’ to J.X. for the preparation of the manuscript; Tianjin Key Medical Discipline (Specialty) Construction Project (grant no. TJYXZDXK-001A to C.Y. for preparation of the manuscript); the National Key R&D Program of China (grant no. 2022YFE0209400 to L.Y. for study design and data analysis); the Tsinghua University Initiative Scientific Research Program (grant no. 2021Z11GHX002 to L.Y. for study design and data analysis); the National Key Scientific and Technological Infrastructure Project ‘Earth System Science Numerical Simulator Facility’ (EarthLab to L.Y. for study design and data analysis); the Chinese National High-end Foreign Expert Recruitment Plan to G.S.; and the Alexander von Humboldt Foundation to G.S. for study design and data analysis. article_processing_charge: No article_type: original author: - first_name: Jiayuan full_name: Xu, Jiayuan last_name: Xu - first_name: Nana full_name: Liu, Nana last_name: Liu - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Liliana full_name: Garcia-Mondragon, Liliana last_name: Garcia-Mondragon - first_name: Jie full_name: Tang, Jie last_name: Tang - first_name: Xiaoxuan full_name: Liu, Xiaoxuan last_name: Liu - first_name: Tristram full_name: Lett, Tristram last_name: Lett - first_name: Le full_name: Yu, Le last_name: Yu - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: Jianfeng full_name: Feng, Jianfeng last_name: Feng - first_name: Chunshui full_name: Yu, Chunshui last_name: Yu - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Henrik full_name: Walter, Henrik last_name: Walter - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Ulrike Helene full_name: Taron, Ulrike Helene last_name: Taron - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Jamie full_name: Banks, Jamie last_name: Banks - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Karina full_name: Jansone, Karina last_name: Jansone - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Sebastian full_name: Siehl, Sebastian last_name: Siehl - first_name: Ole full_name: A. Andreassen, Ole last_name: A. Andreassen - first_name: Lars full_name: T. Westlye, Lars last_name: T. Westlye - first_name: Dennis full_name: Van Der Meer, Dennis last_name: Van Der Meer - first_name: Sara full_name: Fernandez, Sara last_name: Fernandez - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Lena full_name: Marr, Lena id: 4406F586-F248-11E8-B48F-1D18A9856A87 last_name: Marr - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Guillem Feixas full_name: Viapiana, Guillem Feixas last_name: Viapiana - first_name: Francisco Eiroa full_name: Orosa, Francisco Eiroa last_name: Orosa - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Alvaro full_name: Pastor, Alvaro last_name: Pastor - first_name: Andreas full_name: Forstner, Andreas last_name: Forstner - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Markus full_name: M. Nöthen, Markus last_name: M. Nöthen - first_name: Andreas full_name: J. Forstner, Andreas last_name: J. Forstner - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Abbi full_name: Miller, Abbi last_name: Miller - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Mona full_name: Boye, Mona last_name: Boye - first_name: Johannes full_name: Wilbertz, Johannes last_name: Wilbertz - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Séverine full_name: Pitel, Séverine last_name: Pitel - first_name: Lisa full_name: Otten, Lisa last_name: Otten - first_name: Anastasios Polykarpos full_name: Athanasiadis, Anastasios Polykarpos last_name: Athanasiadis - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Elena full_name: Alvarez, Elena last_name: Alvarez - first_name: Mavi full_name: Sanchez, Mavi last_name: Sanchez - first_name: Arantxa full_name: Giner, Arantxa last_name: Giner - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Yanting full_name: Gong, Yanting last_name: Gong - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Vince full_name: Calhoun, Vince last_name: Calhoun - first_name: Jingyu full_name: Liu, Jingyu last_name: Liu - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Sylvane full_name: Desrivieres, Sylvane last_name: Desrivieres - first_name: Allan full_name: H. Young, Allan last_name: H. Young - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: George full_name: Ogoh, George last_name: Ogoh citation: ama: Xu J, Liu N, Polemiti E, et al. Effects of urban living environments on mental health in adults. Nature Medicine. 2023;29:1456-1467. doi:10.1038/s41591-023-02365-w apa: Xu, J., Liu, N., Polemiti, E., Garcia-Mondragon, L., Tang, J., Liu, X., … Ogoh, G. (2023). Effects of urban living environments on mental health in adults. Nature Medicine. Springer Nature. https://doi.org/10.1038/s41591-023-02365-w chicago: Xu, Jiayuan, Nana Liu, Elli Polemiti, Liliana Garcia-Mondragon, Jie Tang, Xiaoxuan Liu, Tristram Lett, et al. “Effects of Urban Living Environments on Mental Health in Adults.” Nature Medicine. Springer Nature, 2023. https://doi.org/10.1038/s41591-023-02365-w. ieee: J. Xu et al., “Effects of urban living environments on mental health in adults,” Nature Medicine, vol. 29. Springer Nature, pp. 1456–1467, 2023. ista: Xu J, Liu N, Polemiti E, Garcia-Mondragon L, Tang J, Liu X, Lett T, Yu L, Nöthen MM, Feng J, Yu C, Marquand A, Schumann G, Walter H, Heinz A, Ralser M, Twardziok S, Vaidya N, Serin E, Jentsch M, Hitchen E, Eils R, Taron UH, Schütz T, Schepanski K, Banks J, Banaschewski T, Jansone K, Christmann N, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Neidhart M, Nees F, Siehl S, A. Andreassen O, T. Westlye L, Van Der Meer D, Fernandez S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Novarino G, Marr L, Slater M, Viapiana GF, Orosa FE, Gallego J, Pastor A, Forstner A, Hoffmann P, M. Nöthen M, J. Forstner A, Claus I, Miller A, Heilmann-Heimbach S, Sommer P, Boye M, Wilbertz J, Schmitt K, Jirsa V, Petkoski S, Pitel S, Otten L, Athanasiadis AP, Pearmund C, Spanlang B, Alvarez E, Sanchez M, Giner A, Hese S, Renner P, Jia T, Gong Y, Xia Y, Chang X, Calhoun V, Liu J, Thompson P, Clinton N, Desrivieres S, H. Young A, Stahl B, Ogoh G. 2023. Effects of urban living environments on mental health in adults. Nature Medicine. 29, 1456–1467. mla: Xu, Jiayuan, et al. “Effects of Urban Living Environments on Mental Health in Adults.” Nature Medicine, vol. 29, Springer Nature, 2023, pp. 1456–67, doi:10.1038/s41591-023-02365-w. short: J. Xu, N. Liu, E. Polemiti, L. Garcia-Mondragon, J. Tang, X. Liu, T. Lett, L. Yu, M.M. Nöthen, J. Feng, C. Yu, A. Marquand, G. Schumann, H. Walter, A. Heinz, M. Ralser, S. Twardziok, N. Vaidya, E. Serin, M. Jentsch, E. Hitchen, R. Eils, U.H. Taron, T. Schütz, K. Schepanski, J. Banks, T. Banaschewski, K. Jansone, N. Christmann, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, M. Neidhart, F. Nees, S. Siehl, O. A. Andreassen, L. T. Westlye, D. Van Der Meer, S. Fernandez, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, G. Novarino, L. Marr, M. Slater, G.F. Viapiana, F.E. Orosa, J. Gallego, A. Pastor, A. Forstner, P. Hoffmann, M. M. Nöthen, A. J. Forstner, I. Claus, A. Miller, S. Heilmann-Heimbach, P. Sommer, M. Boye, J. Wilbertz, K. Schmitt, V. Jirsa, S. Petkoski, S. Pitel, L. Otten, A.P. Athanasiadis, C. Pearmund, B. Spanlang, E. Alvarez, M. Sanchez, A. Giner, S. Hese, P. Renner, T. Jia, Y. Gong, Y. Xia, X. Chang, V. Calhoun, J. Liu, P. Thompson, N. Clinton, S. Desrivieres, A. H. Young, B. Stahl, G. Ogoh, Nature Medicine 29 (2023) 1456–1467. date_created: 2023-06-25T22:00:46Z date_published: 2023-06-15T00:00:00Z date_updated: 2023-12-13T11:25:55Z day: '15' ddc: - '570' department: - _id: GaNo doi: 10.1038/s41591-023-02365-w external_id: isi: - '001013172700001' file: - access_level: open_access checksum: bcd3225b2731c3442fa98987fd3bd46d content_type: application/pdf creator: dernst date_created: 2023-06-26T10:15:44Z date_updated: 2023-06-26T10:15:44Z file_id: '13171' file_name: 2023_NatureMedicine_Xu.pdf file_size: 7365360 relation: main_file success: 1 file_date_updated: 2023-06-26T10:15:44Z has_accepted_license: '1' intvolume: ' 29' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1456-1467 publication: Nature Medicine publication_identifier: eissn: - 1546-170X issn: - 1078-8956 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Effects of urban living environments on mental health in adults 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: 29 year: '2023' ... --- _id: '12976' abstract: - lang: eng text: "3D printing based on continuous deposition of materials, such as filament-based 3D printing, has seen widespread adoption thanks to its versatility in working with a wide range of materials. An important shortcoming of this type of technology is its limited multi-material capabilities. While there are simple hardware designs that enable multi-material printing in principle, the required software is heavily underdeveloped. A typical hardware design fuses together individual materials fed into a single chamber from multiple inlets before they are deposited. This design, however, introduces a time delay between the intended material mixture and its actual deposition. In this work, inspired by diverse path planning research in robotics, we show that this mechanical challenge can be addressed via improved printer control. We propose to formulate the search for optimal multi-material printing policies in a reinforcement\r\nlearning setup. We put forward a simple numerical deposition model that takes into account the non-linear material mixing and delayed material deposition. To validate our system we focus on color fabrication, a problem known for its strict requirements for varying material mixtures at a high spatial frequency. We demonstrate that our learned control policy outperforms state-of-the-art hand-crafted algorithms." acknowledgement: This work is graciously supported by FWF Lise Meitner (Grant M 3319). Kang Liao sincerely thank Emiliano Luci, Chunyu Lin, and Yao Zhao for their huge support. article_processing_charge: No author: - first_name: Kang full_name: Liao, Kang last_name: Liao - first_name: Thibault full_name: Tricard, Thibault last_name: Tricard - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Hans-Peter full_name: Seidel, Hans-Peter last_name: Seidel - first_name: Vahid full_name: Babaei, Vahid last_name: Babaei citation: ama: 'Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. Learning deposition policies for fused multi-material 3D printing. In: 2023 IEEE International Conference on Robotics and Automation. Vol 2023. IEEE; 2023:12345-12352. doi:10.1109/ICRA48891.2023.10160465' apa: 'Liao, K., Tricard, T., Piovarci, M., Seidel, H.-P., & Babaei, V. (2023). Learning deposition policies for fused multi-material 3D printing. In 2023 IEEE International Conference on Robotics and Automation (Vol. 2023, pp. 12345–12352). London, United Kingdom: IEEE. https://doi.org/10.1109/ICRA48891.2023.10160465' chicago: Liao, Kang, Thibault Tricard, Michael Piovarci, Hans-Peter Seidel, and Vahid Babaei. “Learning Deposition Policies for Fused Multi-Material 3D Printing.” In 2023 IEEE International Conference on Robotics and Automation, 2023:12345–52. IEEE, 2023. https://doi.org/10.1109/ICRA48891.2023.10160465. ieee: K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, and V. Babaei, “Learning deposition policies for fused multi-material 3D printing,” in 2023 IEEE International Conference on Robotics and Automation, London, United Kingdom, 2023, vol. 2023, pp. 12345–12352. ista: 'Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. 2023. Learning deposition policies for fused multi-material 3D printing. 2023 IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation vol. 2023, 12345–12352.' mla: Liao, Kang, et al. “Learning Deposition Policies for Fused Multi-Material 3D Printing.” 2023 IEEE International Conference on Robotics and Automation, vol. 2023, IEEE, 2023, pp. 12345–52, doi:10.1109/ICRA48891.2023.10160465. short: K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, V. Babaei, in:, 2023 IEEE International Conference on Robotics and Automation, IEEE, 2023, pp. 12345–12352. conference: end_date: 2023-06-02 location: London, United Kingdom name: 'ICRA: International Conference on Robotics and Automation' start_date: 2023-05-29 date_created: 2023-05-16T09:14:09Z date_published: 2023-07-04T00:00:00Z date_updated: 2023-12-13T11:20:00Z day: '04' ddc: - '004' department: - _id: BeBi doi: 10.1109/ICRA48891.2023.10160465 external_id: isi: - '001048371104068' file: - access_level: open_access checksum: daeaa67124777d88487f933ea3f77164 content_type: application/pdf creator: mpiovarc date_created: 2023-05-16T09:12:05Z date_updated: 2023-05-16T09:12:05Z file_id: '12977' file_name: Liao2023.pdf file_size: 5367986 relation: main_file success: 1 file_date_updated: 2023-05-16T09:12:05Z has_accepted_license: '1' intvolume: ' 2023' isi: 1 keyword: - reinforcement learning - deposition - control - color - multi-filament language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 12345-12352 project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication publication: 2023 IEEE International Conference on Robotics and Automation publication_identifier: eisbn: - '9798350323658' issn: - 1050-4729 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Learning deposition policies for fused multi-material 3D printing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '13164' abstract: - lang: eng text: Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization. acknowledgement: We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission. article_number: '3506' article_processing_charge: No article_type: original author: - first_name: Krista R.B. full_name: Gert, Krista R.B. last_name: Gert - first_name: Karin full_name: Panser, Karin last_name: Panser - first_name: Joachim full_name: Surm, Joachim last_name: Surm - first_name: Benjamin S. full_name: Steinmetz, Benjamin S. last_name: Steinmetz - first_name: Alexander full_name: Schleiffer, Alexander last_name: Schleiffer - first_name: Luca full_name: Jovine, Luca last_name: Jovine - first_name: Yehu full_name: Moran, Yehu last_name: Moran - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Andrea full_name: Pauli, Andrea last_name: Pauli citation: ama: Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 2023;14. doi:10.1038/s41467-023-39317-4 apa: Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39317-4 chicago: Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39317-4. ieee: K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506. mla: Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications, vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4. short: K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023). date_created: 2023-06-25T22:00:45Z date_published: 2023-06-14T00:00:00Z date_updated: 2023-12-13T11:26:34Z day: '14' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41467-023-39317-4 external_id: isi: - '001048208600023' file: - access_level: open_access checksum: d6165f41c7f1c2c04b04256ec9f003fb content_type: application/pdf creator: dernst date_created: 2023-06-26T10:26:04Z date_updated: 2023-06-26T10:26:04Z file_id: '13172' file_name: 2023_NatureComm_Gert.pdf file_size: 1555006 relation: main_file success: 1 file_date_updated: 2023-06-26T10:26:04Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries 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: '12313' abstract: - lang: eng text: Let P be a nontorsion point on an elliptic curve defined over a number field K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that every term of the sequence of the Bn has a primitive divisor for n greater than an effectively computable constant that we will explicitly compute. This constant will depend only on the model defining the curve. acknowledgement: "This paper is part of the author’s PhD thesis at Università of Pisa. Moreover, this\r\nproject has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement\r\nNo. 101034413. I thank the referee for many helpful comments." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Matteo full_name: Verzobio, Matteo id: 7aa8f170-131e-11ed-88e1-a9efd01027cb last_name: Verzobio orcid: 0000-0002-0854-0306 citation: ama: Verzobio M. Some effectivity results for primitive divisors of elliptic divisibility  sequences. Pacific Journal of Mathematics. 2023;325(2):331-351. doi:10.2140/pjm.2023.325.331 apa: Verzobio, M. (2023). Some effectivity results for primitive divisors of elliptic divisibility  sequences. Pacific Journal of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.325.331 chicago: Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility  Sequences.” Pacific Journal of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.325.331. ieee: M. Verzobio, “Some effectivity results for primitive divisors of elliptic divisibility  sequences,” Pacific Journal of Mathematics, vol. 325, no. 2. Mathematical Sciences Publishers, pp. 331–351, 2023. ista: Verzobio M. 2023. Some effectivity results for primitive divisors of elliptic divisibility  sequences. Pacific Journal of Mathematics. 325(2), 331–351. mla: Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility  Sequences.” Pacific Journal of Mathematics, vol. 325, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–51, doi:10.2140/pjm.2023.325.331. short: M. Verzobio, Pacific Journal of Mathematics 325 (2023) 331–351. date_created: 2023-01-16T11:46:19Z date_published: 2023-11-03T00:00:00Z date_updated: 2023-12-13T11:18:14Z day: '03' ddc: - '510' department: - _id: TiBr doi: 10.2140/pjm.2023.325.331 ec_funded: 1 external_id: arxiv: - '2001.02987' isi: - '001104766900001' file: - access_level: open_access checksum: b6218d16a72742d8bb38d6fc3c9bb8c6 content_type: application/pdf creator: dernst date_created: 2023-11-13T09:50:41Z date_updated: 2023-11-13T09:50:41Z file_id: '14525' file_name: 2023_PacificJourMaths_Verzobio.pdf file_size: 389897 relation: main_file success: 1 file_date_updated: 2023-11-13T09:50:41Z has_accepted_license: '1' intvolume: ' 325' isi: 1 issue: '2' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 331-351 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Pacific Journal of Mathematics publication_identifier: eissn: - 0030-8730 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Some effectivity results for primitive divisors of elliptic divisibility sequences 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: 325 year: '2023' ... --- _id: '13145' abstract: - lang: eng text: We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes. acknowledgement: Research supported by the Sfb 1060 The Mathematics of Emergent Effects (University of Bonn). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through project ESPRIT 208. article_processing_charge: No article_type: original author: - first_name: Lorenzo full_name: Dello Schiavo, Lorenzo id: ECEBF480-9E4F-11EA-B557-B0823DDC885E last_name: Dello Schiavo orcid: 0000-0002-9881-6870 - first_name: Eugene full_name: Lytvynov, Eugene last_name: Lytvynov citation: ama: Dello Schiavo L, Lytvynov E. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 2023;28:1-12. doi:10.1214/23-ECP528 apa: Dello Schiavo, L., & Lytvynov, E. (2023). A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-ECP528 chicago: Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP528. ieee: L. Dello Schiavo and E. Lytvynov, “A Mecke-type characterization of the Dirichlet–Ferguson measure,” Electronic Communications in Probability, vol. 28. Institute of Mathematical Statistics, pp. 1–12, 2023. ista: Dello Schiavo L, Lytvynov E. 2023. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 28, 1–12. mla: Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–12, doi:10.1214/23-ECP528. short: L. Dello Schiavo, E. Lytvynov, Electronic Communications in Probability 28 (2023) 1–12. date_created: 2023-06-18T22:00:48Z date_published: 2023-05-05T00:00:00Z date_updated: 2023-12-13T11:24:57Z day: '05' ddc: - '510' department: - _id: JaMa doi: 10.1214/23-ECP528 external_id: isi: - '001042025400001' file: - access_level: open_access checksum: 4a543fe4b3f9e747cc52167c17bfb524 content_type: application/pdf creator: dernst date_created: 2023-06-19T09:37:40Z date_updated: 2023-06-19T09:37:40Z file_id: '13152' file_name: 2023_ElectronCommProbability_Schiavo.pdf file_size: 271434 relation: main_file success: 1 file_date_updated: 2023-06-19T09:37:40Z has_accepted_license: '1' intvolume: ' 28' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1-12 project: - _id: 34dbf174-11ca-11ed-8bc3-afe9d43d4b9c grant_number: E208 name: Configuration Spaces over Non-Smooth Spaces 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: A Mecke-type characterization of the Dirichlet–Ferguson measure 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: '12838' abstract: - lang: eng text: We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L – 1 balls of radius √ nN around points in C . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. acknowledgement: "YZ thanks Jiajin Li for making the observation given by Equation (23). He also would like to thank Nir Ailon and Ely Porat for several helpful conversations throughout this project, and Alexander Barg for insightful comments on the manuscript.\r\nYZ has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]. The work of SV was supported by a seed grant from IIT Hyderabad and the start-up research grant from the Science and Engineering Research Board, India (SRG/2020/000910)." article_processing_charge: No article_type: original author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 - first_name: Shashank full_name: Vatedka, Shashank last_name: Vatedka citation: ama: 'Zhang Y, Vatedka S. Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. 2023;69(7):4513-4527. doi:10.1109/TIT.2023.3260950' apa: 'Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3260950' chicago: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” IEEE Transactions on Information Theory. IEEE, 2023. https://doi.org/10.1109/TIT.2023.3260950.' ieee: 'Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via infinite constellations,” IEEE Transactions on Information Theory, vol. 69, no. 7. IEEE, pp. 4513–4527, 2023.' ista: 'Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. 69(7), 4513–4527.' mla: 'Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” IEEE Transactions on Information Theory, vol. 69, no. 7, IEEE, 2023, pp. 4513–27, doi:10.1109/TIT.2023.3260950.' short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 69 (2023) 4513–4527. date_created: 2023-04-16T22:01:09Z date_published: 2023-07-01T00:00:00Z date_updated: 2023-12-13T11:16:46Z day: '01' department: - _id: MaMo doi: 10.1109/TIT.2023.3260950 external_id: arxiv: - '2211.04407' isi: - '001017307000023' intvolume: ' 69' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2211.04407 month: '07' oa: 1 oa_version: Preprint page: 4513-4527 publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Multiple packing: Lower bounds via infinite constellations' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2023' ... --- _id: '13228' abstract: - lang: eng text: A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox. acknowledgement: 'The authors would like to thank the anonymous reviewers for their valuable comments and helpful suggestions. This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.' 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: Mahyar full_name: Karimi, Mahyar last_name: Karimi - 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, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic fairness properties. In: FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. Association for Computing Machinery; 2023:604-614. doi:10.1145/3593013.3594028' apa: 'Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Runtime monitoring of dynamic fairness properties. In FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency (pp. 604–614). Chicago, IL, United States: Association for Computing Machinery. https://doi.org/10.1145/3593013.3594028' chicago: 'Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Runtime Monitoring of Dynamic Fairness Properties.” In FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, 604–14. Association for Computing Machinery, 2023. https://doi.org/10.1145/3593013.3594028.' ieee: 'T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring of dynamic fairness properties,” in FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Chicago, IL, United States, 2023, pp. 604–614.' ista: 'Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness, Accountability and Transparency, 604–614.' mla: 'Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.” FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–14, doi:10.1145/3593013.3594028.' short: 'T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–614.' conference: end_date: 2023-06-15 location: Chicago, IL, United States name: 'FAccT: Conference on Fairness, Accountability and Transparency' start_date: 2023-06-12 date_created: 2023-07-16T22:01:09Z date_published: 2023-06-12T00:00:00Z date_updated: 2023-12-13T11:30:31Z day: '12' ddc: - '000' department: - _id: ToHe doi: 10.1145/3593013.3594028 ec_funded: 1 external_id: arxiv: - '2305.04699' isi: - '001062819300057' file: - access_level: open_access checksum: 96c759db9cdf94b81e37871a66a6ff48 content_type: application/pdf creator: dernst date_created: 2023-07-18T07:43:10Z date_updated: 2023-07-18T07:43:10Z file_id: '13245' file_name: 2023_ACM_HenzingerT.pdf file_size: 4100596 relation: main_file success: 1 file_date_updated: 2023-07-18T07:43:10Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 604-614 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 'FAccT ''23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency' publication_identifier: isbn: - '9781450372527' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Runtime monitoring of dynamic fairness properties 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 year: '2023' ... --- _id: '13225' abstract: - lang: eng text: Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy. acknowledgement: "RS was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227). MP acknowledges financial support from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, Grant Agreement No. 802901). BS acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC AdG CLaQS (Grant Agreement No. 834782). NB and MP were supported by Gruppo Nazionale per la Fisica Matematica (GNFM) of Italy. NB was supported by the European Research Council’s Starting Grant FERMIMATH (Grant Agreement No. 101040991).\r\nOpen access funding provided by Università degli Studi di Milano within the CRUI-CARE Agreement." article_number: '65' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Niels P full_name: Benedikter, Niels P id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87 last_name: Benedikter orcid: 0000-0002-1071-6091 - first_name: Marcello full_name: Porta, Marcello last_name: Porta - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Benedikter NP, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 2023;247(4). doi:10.1007/s00205-023-01893-6 apa: Benedikter, N. P., Porta, M., Schlein, B., & Seiringer, R. (2023). Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01893-6 chicago: Benedikter, Niels P, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01893-6. ieee: N. P. Benedikter, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas with large interaction potential,” Archive for Rational Mechanics and Analysis, vol. 247, no. 4. Springer Nature, 2023. ista: Benedikter NP, Porta M, Schlein B, Seiringer R. 2023. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 247(4), 65. mla: Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” Archive for Rational Mechanics and Analysis, vol. 247, no. 4, 65, Springer Nature, 2023, doi:10.1007/s00205-023-01893-6. short: N.P. Benedikter, M. Porta, B. Schlein, R. Seiringer, Archive for Rational Mechanics and Analysis 247 (2023). date_created: 2023-07-16T22:01:08Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T11:31:14Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00205-023-01893-6 ec_funded: 1 external_id: arxiv: - '2106.13185' isi: - '001024369000001' file: - access_level: open_access checksum: 2b45828d854a253b14bf7aa196ec55e9 content_type: application/pdf creator: dernst date_created: 2023-11-14T13:12:12Z date_updated: 2023-11-14T13:12:12Z file_id: '14535' file_name: 2023_ArchiveRationalMechAnalysis_Benedikter.pdf file_size: 851626 relation: main_file success: 1 file_date_updated: 2023-11-14T13:12:12Z has_accepted_license: '1' intvolume: ' 247' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Correlation energy of a weakly interacting Fermi gas with large interaction potential 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: 247 year: '2023' ... --- _id: '13226' abstract: - lang: eng text: We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion. acknowledgement: "It is a pleasure to thank Martin Kolb, Simone Rademacher, Robert Seiringer and Stefan Teufel for helpful discussions. Moreover, we thank the referee for many constructive comments. L.B. gratefully acknowledges funding from the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We thank the Mathematical Research Institute Oberwolfach, where part of this work was done, for their hospitality.\r\nOpen Access funding enabled and organized by Projekt DEAL." article_number: '77' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lea full_name: Bossmann, Lea id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425 last_name: Bossmann orcid: 0000-0002-6854-1343 - first_name: Sören P full_name: Petrat, Sören P id: 40AC02DC-F248-11E8-B48F-1D18A9856A87 last_name: Petrat orcid: 0000-0002-9166-5889 citation: ama: Bossmann L, Petrat SP. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 2023;113(4). doi:10.1007/s11005-023-01698-4 apa: Bossmann, L., & Petrat, S. P. (2023). Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-023-01698-4 chicago: Bossmann, Lea, and Sören P Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” Letters in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s11005-023-01698-4. ieee: L. Bossmann and S. P. Petrat, “Weak Edgeworth expansion for the mean-field Bose gas,” Letters in Mathematical Physics, vol. 113, no. 4. Springer Nature, 2023. ista: Bossmann L, Petrat SP. 2023. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 113(4), 77. mla: Bossmann, Lea, and Sören P. Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” Letters in Mathematical Physics, vol. 113, no. 4, 77, Springer Nature, 2023, doi:10.1007/s11005-023-01698-4. short: L. Bossmann, S.P. Petrat, Letters in Mathematical Physics 113 (2023). date_created: 2023-07-16T22:01:08Z date_published: 2023-07-03T00:00:00Z date_updated: 2023-12-13T11:31:50Z day: '03' department: - _id: RoSe doi: 10.1007/s11005-023-01698-4 ec_funded: 1 external_id: arxiv: - '2208.00199' isi: - '001022878900002' intvolume: ' 113' isi: 1 issue: '4' language: - iso: eng month: '07' oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Letters in Mathematical Physics publication_identifier: eissn: - 1573-0530 issn: - 0377-9017 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Weak Edgeworth expansion for the mean-field Bose gas type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2023' ... --- _id: '13227' abstract: - lang: eng text: Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: The authors thank J. Koch for discussions and support with the scQubits python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA workshop and the IST nanofabrication facility for technical contributions, as well as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the prompt support of Quantum Machines to implement active state preparation with their OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria. article_number: '3968' article_processing_charge: No article_type: original author: - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Lucky full_name: Kapoor, Lucky id: 84b9700b-15b2-11ec-abd3-831089e67615 last_name: Kapoor - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - 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: Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 2023;14. doi:10.1038/s41467-023-39656-2 apa: Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., & Fink, J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39656-2 chicago: Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka, and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39656-2. ieee: F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink, “Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 14, 3968. mla: Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications, vol. 14, 3968, Springer Nature, 2023, doi:10.1038/s41467-023-39656-2. short: F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature Communications 14 (2023). date_created: 2023-07-16T22:01:08Z date_published: 2023-07-05T00:00:00Z date_updated: 2023-12-13T11:32:25Z day: '05' ddc: - '530' department: - _id: JoFi doi: 10.1038/s41467-023-39656-2 external_id: isi: - '001024729900009' pmid: - '37407570' file: - access_level: open_access checksum: a85773b5fe23516f60f7d5d31b55c200 content_type: application/pdf creator: dernst date_created: 2023-07-18T08:43:07Z date_updated: 2023-07-18T08:43:07Z file_id: '13248' file_name: 2023_NatureComm_Hassani.pdf file_size: 2899592 relation: main_file success: 1 file_date_updated: 2023-07-18T08:43:07Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 2622978C-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours 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: '13321' abstract: - lang: eng text: We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm. acknowledgement: Marco Mondelli was partially supported by the 2019 Lopez-Loreta prize. article_processing_charge: No author: - first_name: Yizhou full_name: Xu, Yizhou last_name: Xu - first_name: Tian Qi full_name: Hou, Tian Qi last_name: Hou - first_name: Shan Suo full_name: Liang, Shan Suo last_name: Liang - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Xu Y, Hou TQ, Liang SS, Mondelli M. Approximate message passing for multi-layer estimation in rotationally invariant models. In: 2023 IEEE Information Theory Workshop. Institute of Electrical and Electronics Engineers; 2023:294-298. doi:10.1109/ITW55543.2023.10160238' apa: 'Xu, Y., Hou, T. Q., Liang, S. S., & Mondelli, M. (2023). Approximate message passing for multi-layer estimation in rotationally invariant models. In 2023 IEEE Information Theory Workshop (pp. 294–298). Saint-Malo, France: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ITW55543.2023.10160238' chicago: Xu, Yizhou, Tian Qi Hou, Shan Suo Liang, and Marco Mondelli. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” In 2023 IEEE Information Theory Workshop, 294–98. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/ITW55543.2023.10160238. ieee: Y. Xu, T. Q. Hou, S. S. Liang, and M. Mondelli, “Approximate message passing for multi-layer estimation in rotationally invariant models,” in 2023 IEEE Information Theory Workshop, Saint-Malo, France, 2023, pp. 294–298. ista: 'Xu Y, Hou TQ, Liang SS, Mondelli M. 2023. Approximate message passing for multi-layer estimation in rotationally invariant models. 2023 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 294–298.' mla: Xu, Yizhou, et al. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–98, doi:10.1109/ITW55543.2023.10160238. short: Y. Xu, T.Q. Hou, S.S. Liang, M. Mondelli, in:, 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–298. conference: end_date: 2023-04-28 location: Saint-Malo, France name: 'ITW: Information Theory Workshop' start_date: 2023-04-23 date_created: 2023-07-30T22:01:04Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-12-13T11:35:46Z day: '01' department: - _id: MaMo doi: 10.1109/ITW55543.2023.10160238 external_id: arxiv: - '2212.01572' isi: - '001031733100053' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2212.01572 month: '05' oa: 1 oa_version: Preprint page: 294-298 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 2023 IEEE Information Theory Workshop publication_identifier: eissn: - 2475-4218 isbn: - '9798350301496' publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Approximate message passing for multi-layer estimation in rotationally invariant models type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13265' abstract: - lang: eng text: In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality. acknowledgement: 'This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ' article_number: '26' article_processing_charge: No article_type: original author: - first_name: Fanchao full_name: Zhong, Fanchao last_name: Zhong - first_name: Yonglai full_name: Xu, Yonglai last_name: Xu - first_name: Haisen full_name: Zhao, Haisen id: fb7f793a-80d1-11eb-8869-d56e5b2a8ff4 last_name: Zhao orcid: 0000-0002-6389-1045 - first_name: Lin full_name: Lu, Lin last_name: Lu citation: ama: Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 2023;42(3). doi:10.1145/3575859 apa: Zhong, F., Xu, Y., Zhao, H., & Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3575859 chicago: Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3575859. ieee: F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” ACM Transactions on Graphics, vol. 42, no. 3. Association for Computing Machinery, 2023. ista: Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26. mla: Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:10.1145/3575859. short: F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023). date_created: 2023-07-23T22:01:13Z date_published: 2023-03-17T00:00:00Z date_updated: 2023-12-13T11:34:59Z day: '17' department: - _id: BeBi doi: 10.1145/3575859 external_id: arxiv: - '2201.02374' isi: - '001018739600002' intvolume: ' 42' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2201.02374 month: '03' oa: 1 oa_version: Preprint publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: As-Continuous-As-Possible extrusion-based fabrication of surface models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '13318' abstract: - lang: eng text: Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes. acknowledgement: The research of A.V. is supported by NSF DMS-1900286, DMS-2154402 and by Hausdorff Center for Mathematics. H.Z. is supported by the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. This work is partially supported by NSF DMS-1929284 while both authors were in residence at the Institute for Computational and Experimental Research in Mathematics in Providence, RI, during the Harmonic Analysis and Convexity program. article_processing_charge: No article_type: original author: - first_name: Alexander full_name: Volberg, Alexander last_name: Volberg - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Volberg A, Zhang H. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. 2023. doi:10.1007/s00208-023-02680-0 apa: Volberg, A., & Zhang, H. (2023). Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-023-02680-0 chicago: Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen. Springer Nature, 2023. https://doi.org/10.1007/s00208-023-02680-0. ieee: A. Volberg and H. Zhang, “Noncommutative Bohnenblust–Hille inequalities,” Mathematische Annalen. Springer Nature, 2023. ista: Volberg A, Zhang H. 2023. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. mla: Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen, Springer Nature, 2023, doi:10.1007/s00208-023-02680-0. short: A. Volberg, H. Zhang, Mathematische Annalen (2023). date_created: 2023-07-30T22:01:03Z date_published: 2023-07-24T00:00:00Z date_updated: 2023-12-13T11:36:20Z day: '24' department: - _id: JaMa doi: 10.1007/s00208-023-02680-0 external_id: arxiv: - '2210.14468' isi: - '001035665500001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00208-023-02680-0 month: '07' oa: 1 oa_version: Published Version project: - _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6 grant_number: M03337 name: Curvature-dimension in noncommutative analysis publication: Mathematische Annalen publication_identifier: eissn: - 1432-1807 issn: - 0025-5831 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Noncommutative Bohnenblust–Hille inequalities type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13271' abstract: - lang: eng text: "In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,\r\nfor parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems." acknowledgement: I am grateful to Boguslaw Zegarliński for asking me the questions in [3] and for helpful communication. I also want to thank Paata Ivanisvili for drawing [25] to my attention and for useful correspondence. Many thanks to the anonymous referee for the valuable comments and for pointing out some errors in an earlier version of the paper. This work is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. article_processing_charge: No article_type: original author: - first_name: Haonan full_name: Zhang, Haonan id: D8F41E38-9E66-11E9-A9E2-65C2E5697425 last_name: Zhang citation: ama: Zhang H. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. 2023. doi:10.1007/s00023-023-01345-7 apa: Zhang, H. (2023). Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-023-01345-7 chicago: Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-023-01345-7. ieee: H. Zhang, “Some convexity and monotonicity results of trace functionals,” Annales Henri Poincare. Springer Nature, 2023. ista: Zhang H. 2023. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. mla: Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare, Springer Nature, 2023, doi:10.1007/s00023-023-01345-7. short: H. Zhang, Annales Henri Poincare (2023). date_created: 2023-07-23T22:01:15Z date_published: 2023-07-08T00:00:00Z date_updated: 2023-12-13T11:33:46Z day: '08' department: - _id: JaMa doi: 10.1007/s00023-023-01345-7 ec_funded: 1 external_id: arxiv: - '2108.05785' isi: - '001025709100001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2108.05785 month: '07' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6 grant_number: M03337 name: Curvature-dimension in noncommutative analysis publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Some convexity and monotonicity results of trace functionals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13258' abstract: - lang: eng text: Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation. acknowledgement: 'This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).' article_number: '4153' article_processing_charge: Yes article_type: original author: - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Stepan full_name: Simsa, Stepan id: 409d615c-2f95-11ee-b934-90a352102c1e last_name: Simsa orcid: 0000-0001-6687-1210 - 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: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 2023;14. doi:10.1038/s41467-023-39625-9 apa: Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., & Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39625-9 chicago: Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39625-9. ieee: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153. mla: Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications, vol. 14, 4153, Springer Nature, 2023, doi:10.1038/s41467-023-39625-9. short: M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023). date_created: 2023-07-23T22:01:11Z date_published: 2023-07-12T00:00:00Z date_updated: 2023-12-13T11:42:38Z day: '12' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41467-023-39625-9 ec_funded: 1 external_id: isi: - '001029450400031' pmid: - '37438341' file: - access_level: open_access checksum: 5aceefdfe76686267b93ae4fe81899f1 content_type: application/pdf creator: dernst date_created: 2023-07-31T11:32:36Z date_updated: 2023-07-31T11:32:36Z file_id: '13337' file_name: 2023_NatureComm_Kleshnina.pdf file_size: 1601682 relation: main_file success: 1 file_date_updated: 2023-07-31T11:32:36Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '07' 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' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13336' relation: research_data status: public scopus_import: '1' status: public title: The effect of environmental information on evolution of cooperation in 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: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '13263' abstract: - lang: eng text: "Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models." acknowledgement: This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413]. article_processing_charge: Yes article_type: original author: - first_name: Van Giang full_name: Trinh, Van Giang last_name: Trinh - first_name: Belaid full_name: Benhamou, Belaid last_name: Benhamou - 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: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 citation: ama: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 2023;39(Supplement_1):i513-i522. doi:10.1093/bioinformatics/btad262' apa: 'Trinh, V. G., Benhamou, B., Henzinger, T. A., & Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad262' chicago: 'Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad262.' ieee: 'V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” Bioinformatics, vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.' ista: 'Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.' mla: 'Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics, vol. 39, no. Supplement_1, Oxford Academic, 2023, pp. i513–22, doi:10.1093/bioinformatics/btad262.' short: V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522. date_created: 2023-07-23T22:01:12Z date_published: 2023-06-30T00:00:00Z date_updated: 2023-12-13T11:41:52Z day: '30' ddc: - '000' department: - _id: ToHe doi: 10.1093/bioinformatics/btad262 ec_funded: 1 external_id: isi: - '001027457000060' pmid: - '37387165' file: - access_level: open_access checksum: ba3abe1171df1958413b7c7f957f5486 content_type: application/pdf creator: dernst date_created: 2023-07-31T11:09:05Z date_updated: 2023-07-31T11:09:05Z file_id: '13335' file_name: 2023_Bioinformatics_Trinh.pdf file_size: 641736 relation: main_file success: 1 file_date_updated: 2023-07-31T11:09:05Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: Supplement_1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: i513-i522 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Bioinformatics publication_identifier: eissn: - 1367-4811 issn: - 1367-4803 publication_status: published publisher: Oxford Academic quality_controlled: '1' related_material: link: - relation: software url: https://github.com/giang-trinh/trap-mvn scopus_import: '1' status: public title: 'Trap spaces of multi-valued networks: Definition, computation, and applications' 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: '13316' abstract: - lang: eng text: Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN. acknowledgement: 'This work was supported by JSPS KAKENHI grant #18K062291, and the Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the Takeda Science Foundation, and Life Science Foundation of Japan to JT.' article_number: e84850 article_processing_charge: Yes article_type: original author: - first_name: Junko Y. full_name: Toshima, Junko Y. last_name: Toshima - first_name: Ayana full_name: Tsukahara, Ayana last_name: Tsukahara - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Takuro full_name: Tojima, Takuro last_name: Tojima - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Akihiko full_name: Nakano, Akihiko last_name: Nakano - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: ama: Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 2023;12. doi:10.7554/eLife.84850 apa: Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano, A., & Toshima, J. (2023). The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.84850 chicago: Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.84850. ieee: J. Y. Toshima et al., “The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network,” eLife, vol. 12. eLife Sciences Publications, 2023. ista: Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima J. 2023. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 12, e84850. mla: Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife, vol. 12, e84850, eLife Sciences Publications, 2023, doi:10.7554/eLife.84850. short: J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano, J. Toshima, ELife 12 (2023). date_created: 2023-07-30T22:01:02Z date_published: 2023-07-21T00:00:00Z date_updated: 2023-12-13T11:37:36Z day: '21' ddc: - '570' department: - _id: DaSi doi: 10.7554/eLife.84850 external_id: isi: - '001035372800001' pmid: - '37477116' file: - access_level: open_access checksum: 2af111a00cf5e3a956f7f0fd13199b15 content_type: application/pdf creator: dernst date_created: 2023-07-31T07:43:00Z date_updated: 2023-07-31T07:43:00Z file_id: '13324' file_name: 2023_eLife_Toshima.pdf file_size: 11980913 relation: main_file success: 1 file_date_updated: 2023-07-31T07:43:00Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network 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: 12 year: '2023' ... --- _id: '13317' abstract: - lang: eng text: We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction. acknowledgement: "LE, JH, and VR were supported by ERC Advanced Grant “RMTBeyond” No. 101020331. SS was supported by KAKENHI Grant Number JP22J14935 from the Japan Society for the Promotion of Science (JSPS) and Forefront Physics and Mathematics Program to Drive Transformation (FoPM), a World-leading Innovative Graduate Study (WINGS) Program, the University of Tokyo.\r\nOpen access funding provided by The University of Tokyo." article_number: '128' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Shoki full_name: Sugimoto, Shoki last_name: Sugimoto - 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: Volodymyr full_name: Riabov, Volodymyr id: 1949f904-edfb-11eb-afb5-e2dfddabb93b last_name: Riabov - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Sugimoto S, Henheik SJ, Riabov V, Erdös L. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 2023;190(7). doi:10.1007/s10955-023-03132-4 apa: Sugimoto, S., Henheik, S. J., Riabov, V., & Erdös, L. (2023). Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-023-03132-4 chicago: Sugimoto, Shoki, Sven Joscha Henheik, Volodymyr Riabov, and László Erdös. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics. Springer Nature, 2023. https://doi.org/10.1007/s10955-023-03132-4. ieee: S. Sugimoto, S. J. Henheik, V. Riabov, and L. Erdös, “Eigenstate thermalisation hypothesis for translation invariant spin systems,” Journal of Statistical Physics, vol. 190, no. 7. Springer Nature, 2023. ista: Sugimoto S, Henheik SJ, Riabov V, Erdös L. 2023. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 190(7), 128. mla: Sugimoto, Shoki, et al. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics, vol. 190, no. 7, 128, Springer Nature, 2023, doi:10.1007/s10955-023-03132-4. short: S. Sugimoto, S.J. Henheik, V. Riabov, L. Erdös, Journal of Statistical Physics 190 (2023). date_created: 2023-07-30T22:01:02Z date_published: 2023-07-21T00:00:00Z date_updated: 2023-12-13T11:38:44Z day: '21' ddc: - '510' - '530' department: - _id: LaEr doi: 10.1007/s10955-023-03132-4 ec_funded: 1 external_id: arxiv: - '2304.04213' isi: - '001035677200002' file: - access_level: open_access checksum: c2ef6b2aecfee1ad6d03fab620507c2c content_type: application/pdf creator: dernst date_created: 2023-07-31T07:49:31Z date_updated: 2023-07-31T07:49:31Z file_id: '13325' file_name: 2023_JourStatPhysics_Sugimoto.pdf file_size: 612755 relation: main_file success: 1 file_date_updated: 2023-07-31T07:49:31Z has_accepted_license: '1' intvolume: ' 190' isi: 1 issue: '7' language: - iso: eng month: '07' 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 publication: Journal of Statistical Physics publication_identifier: eissn: - 1572-9613 issn: - 0022-4715 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Eigenstate thermalisation hypothesis for translation invariant spin 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: 190 year: '2023' ... --- _id: '13278' abstract: - lang: eng text: We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity "breaks" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms. article_number: '006' article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Rammelmüller, Lukas last_name: Rammelmüller - first_name: David full_name: Huber, David last_name: Huber - first_name: Matija full_name: Čufar, Matija last_name: Čufar - first_name: Joachim full_name: Brand, Joachim last_name: Brand - first_name: Hans-Werner full_name: Hammer, Hans-Werner last_name: Hammer - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 2023;14(1). doi:10.21468/scipostphys.14.1.006 apa: Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., & Volosniev, A. (2023). Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.14.1.006 chicago: Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.14.1.006. ieee: L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev, “Magnetic impurity in a one-dimensional few-fermion system,” SciPost Physics, vol. 14, no. 1. SciPost Foundation, 2023. ista: Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1), 006. mla: Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics, vol. 14, no. 1, 006, SciPost Foundation, 2023, doi:10.21468/scipostphys.14.1.006. short: L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev, SciPost Physics 14 (2023). date_created: 2023-07-24T10:48:23Z date_published: 2023-01-24T00:00:00Z date_updated: 2023-12-13T11:39:32Z day: '24' ddc: - '530' department: - _id: MiLe doi: 10.21468/scipostphys.14.1.006 external_id: arxiv: - '2204.01606' isi: - '001000325800008' file: - access_level: open_access checksum: ffdb70b9ae7aa45ea4ea6096ecbd6431 content_type: application/pdf creator: dernst date_created: 2023-07-31T08:44:38Z date_updated: 2023-07-31T08:44:38Z file_id: '13328' file_name: 2023_SciPostPhysics_Rammelmueller.pdf file_size: 1163444 relation: main_file success: 1 file_date_updated: 2023-07-31T08:44:38Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '1' keyword: - General Physics and Astronomy language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: SciPost Physics publication_identifier: issn: - 2542-4653 publication_status: published publisher: SciPost Foundation quality_controlled: '1' scopus_import: '1' status: public title: Magnetic impurity in a one-dimensional few-fermion system 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: '13274' abstract: - lang: eng text: Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics. acknowledgement: We thank Baofang Song as well as the developers of Channelflow for sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful discussions. This work was supported by a grant from the Simons Foundation (662960, B. H.). article_number: '034002' article_processing_charge: No article_type: original author: - first_name: Chaitanya S full_name: Paranjape, Chaitanya S id: 3D85B7C4-F248-11E8-B48F-1D18A9856A87 last_name: Paranjape - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 - first_name: Yohann full_name: Duguet, Yohann last_name: Duguet - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002 apa: Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023). Direct path from turbulence to time-periodic solutions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.131.034002 chicago: Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002. ieee: C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” Physical Review Letters, vol. 131, no. 3. American Physical Society, 2023. ista: Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002. mla: Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:10.1103/physrevlett.131.034002. short: C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023). date_created: 2023-07-24T09:43:59Z date_published: 2023-07-21T00:00:00Z date_updated: 2023-12-13T11:40:19Z day: '21' department: - _id: GradSch - _id: BjHo doi: 10.1103/physrevlett.131.034002 external_id: arxiv: - '2306.05098' isi: - '001052929900004' intvolume: ' 131' isi: 1 issue: '3' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.05098 month: '07' oa: 1 oa_version: Preprint project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Direct path from turbulence to time-periodic solutions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2023' ... --- _id: '13261' abstract: - lang: eng text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression. acknowledgement: This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship. article_processing_charge: No article_type: original author: - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Hongtao full_name: Chen, Hongtao last_name: Chen - first_name: Lev full_name: Barinov, Lev last_name: Barinov - first_name: Benjamin full_name: Zoller, Benjamin last_name: Zoller - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor citation: ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 2023;380(6652):1357-1362. doi:10.1126/science.adf5568 apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adf5568 chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568. ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” Science, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023. ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362. mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:10.1126/science.adf5568. short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362. date_created: 2023-07-23T22:01:12Z date_published: 2023-06-29T00:00:00Z date_updated: 2023-12-13T11:41:07Z day: '29' department: - _id: EdHa doi: 10.1126/science.adf5568 external_id: isi: - '001106405600028' intvolume: ' 380' isi: 1 issue: '6652' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/science.adf5568 month: '06' oa: 1 oa_version: Preprint page: 1357-1362 project: - _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b grant_number: 343-2022 name: A mechano-chemical theory for stem cell fate decisions in organoid development publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 380 year: '2023' ... --- _id: '13336' article_processing_charge: No author: - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina citation: ama: 'Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564' apa: 'Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564' chicago: 'Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564.' ieee: 'M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.' ista: 'Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564.' mla: 'Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023, doi:10.5281/ZENODO.8059564.' short: M. Kleshnina, (2023). date_created: 2023-07-31T11:30:46Z date_published: 2023-06-20T00:00:00Z date_updated: 2023-12-13T11:42:37Z day: '20' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.8059564 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8059564 month: '06' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13258' relation: used_in_publication status: public status: public title: 'kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13443' abstract: - lang: eng text: 'The ages of solar-like stars have been at the center of many studies such as exoplanet characterization or Galactic-archeology. While ages are usually computed from stellar evolution models, relations linking ages to other stellar properties, such as rotation and magnetic activity, have been investigated. With the large catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index, Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology relations. Stellar ages are obtained with two stellar evolution codes that include treatment of angular momentum evolution, hence using Prot as input in addition to classical atmospheric parameters. We explore two different ways of predicting stellar ages on three subsamples with spectroscopic observations: solar analogs, late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive relations between Sph and ages between 1 and 5 Gyr, and other stellar properties. For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the model with Prot and Sph with median differences of 0.1% and 0.2%, respectively. We also apply Machine Learning techniques with a Random Forest algorithm to predict ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs together, predicted ages are on average within 5.3% of the model ages and improve to 3.1% when including Prot. These are very promising results for a quick age estimation for solar-like stars with photometric observations, especially with current and future space missions.' acknowledgement: 'This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the NASA Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555. We acknowledge that this research was supported in part by the National Science Foundation under grant No. NSF PHY-1748958. S.M. acknowledges support from the Spanish Ministry of Science and Innovation (MICINN) with the Ramón y Cajal fellowship No. RYC-2015-17697, the grant No. PID2019-107061GB-C66, and through AEI under the Severo Ochoa Centres of Excellence Programme 2020–2023 (CEX2019-000920-S). S.M. and D.G.R. acknowledge support from the Spanish Ministry of Science and Innovation (MICINN) with the grant No. PID2019-107187GB-I00. Z.R.C. acknowledges support from National Aeronautics and Space Administration via the TESS Guest Investigator Program (grant No. 80NSSC18K18584). The work presented here was partially supported by the NASA grant NNX17AF27G. A.R.G.S. acknowledges the support by FCT through national funds and by FEDER through COMPETE2020 by the following grants: UIDB/04434/2020 and UIDP/04434/2020. A.R.G.S. is supported by FCT through the work contract No. 2020.02480.CEECIND/CP1631/CT0001. R.A.G., L.A., and S.N.B. acknowledge the support from PLATO and GOLF CNES grants. S.N.B. acknowledges support from PLATO ASI-INAF agreement No. 2015-019-R.1-2018.' article_number: '131' article_processing_charge: Yes article_type: original author: - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Zachary R. full_name: Claytor, Zachary R. last_name: Claytor - first_name: Ângela R. G. full_name: Santos, Ângela R. G. last_name: Santos - first_name: Rafael A. full_name: García, Rafael A. last_name: García - first_name: Louis full_name: Amard, Louis last_name: Amard - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: Enrico full_name: Corsaro, Enrico last_name: Corsaro - first_name: Alfio full_name: Bonanno, Alfio last_name: Bonanno - first_name: Sylvain N. full_name: Breton, Sylvain N. last_name: Breton - first_name: Diego full_name: Godoy-Rivera, Diego last_name: Godoy-Rivera - first_name: Marc H. full_name: Pinsonneault, Marc H. last_name: Pinsonneault - first_name: Jennifer full_name: van Saders, Jennifer last_name: van Saders citation: ama: Mathur S, Claytor ZR, Santos ÂRG, et al. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 2023;952(2). doi:10.3847/1538-4357/acd118 apa: Mathur, S., Claytor, Z. R., Santos, Â. R. G., García, R. A., Amard, L., Bugnet, L. A., … van Saders, J. (2023). Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/acd118 chicago: Mathur, Savita, Zachary R. Claytor, Ângela R. G. Santos, Rafael A. García, Louis Amard, Lisa Annabelle Bugnet, Enrico Corsaro, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/acd118. ieee: S. Mathur et al., “Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations,” The Astrophysical Journal, vol. 952, no. 2. American Astronomical Society, 2023. ista: Mathur S, Claytor ZR, Santos ÂRG, García RA, Amard L, Bugnet LA, Corsaro E, Bonanno A, Breton SN, Godoy-Rivera D, Pinsonneault MH, van Saders J. 2023. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 952(2), 131. mla: Mathur, Savita, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal, vol. 952, no. 2, 131, American Astronomical Society, 2023, doi:10.3847/1538-4357/acd118. short: S. Mathur, Z.R. Claytor, Â.R.G. Santos, R.A. García, L. Amard, L.A. Bugnet, E. Corsaro, A. Bonanno, S.N. Breton, D. Godoy-Rivera, M.H. Pinsonneault, J. van Saders, The Astrophysical Journal 952 (2023). date_created: 2023-08-01T14:19:16Z date_published: 2023-08-01T00:00:00Z date_updated: 2023-12-13T12:00:15Z day: '01' ddc: - '520' department: - _id: LiBu doi: 10.3847/1538-4357/acd118 external_id: isi: - '001034185700001' file: - access_level: open_access checksum: f12452834d7ed6748dbf5ace18af4723 content_type: application/pdf creator: dernst date_created: 2023-08-02T07:42:26Z date_updated: 2023-08-02T07:42:26Z file_id: '13448' file_name: 2023_AstrophysicalJour_Mathur.pdf file_size: 4192386 relation: main_file success: 1 file_date_updated: 2023-08-02T07:42:26Z has_accepted_license: '1' intvolume: ' 952' isi: 1 issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: American Astronomical Society quality_controlled: '1' status: public title: Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations 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: 952 year: '2023' ...