--- _id: '10862' abstract: - lang: eng text: We consider the sum of two large Hermitian matrices A and B with a Haar unitary conjugation bringing them into a general relative position. We prove that the eigenvalue density on the scale slightly above the local eigenvalue spacing is asymptotically given by the free additive convolution of the laws of A and B as the dimension of the matrix increases. This implies optimal rigidity of the eigenvalues and optimal rate of convergence in Voiculescu's theorem. Our previous works [4], [5] established these results in the bulk spectrum, the current paper completely settles the problem at the spectral edges provided they have the typical square-root behavior. The key element of our proof is to compensate the deterioration of the stability of the subordination equations by sharp error estimates that properly account for the local density near the edge. Our results also hold if the Haar unitary matrix is replaced by the Haar orthogonal matrix. acknowledgement: Partially supported by ERC Advanced Grant RANMAT No. 338804. article_number: '108639' article_processing_charge: No article_type: original author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Kevin full_name: Schnelli, Kevin last_name: Schnelli citation: ama: Bao Z, Erdös L, Schnelli K. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 2020;279(7). doi:10.1016/j.jfa.2020.108639 apa: Bao, Z., Erdös, L., & Schnelli, K. (2020). Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2020.108639 chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis. Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108639. ieee: Z. Bao, L. Erdös, and K. Schnelli, “Spectral rigidity for addition of random matrices at the regular edge,” Journal of Functional Analysis, vol. 279, no. 7. Elsevier, 2020. ista: Bao Z, Erdös L, Schnelli K. 2020. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 279(7), 108639. mla: Bao, Zhigang, et al. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis, vol. 279, no. 7, 108639, Elsevier, 2020, doi:10.1016/j.jfa.2020.108639. short: Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 279 (2020). date_created: 2022-03-18T10:18:59Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-08-24T14:08:42Z day: '15' department: - _id: LaEr doi: 10.1016/j.jfa.2020.108639 ec_funded: 1 external_id: arxiv: - '1708.01597' isi: - '000559623200009' intvolume: ' 279' isi: 1 issue: '7' keyword: - Analysis language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.01597 month: '10' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Journal of Functional Analysis publication_identifier: issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Spectral rigidity for addition of random matrices at the regular edge type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 279 year: '2020' ... --- _id: '10867' abstract: - lang: eng text: In this paper we find a tight estimate for Gromov’s waist of the balls in spaces of constant curvature, deduce the estimates for the balls in Riemannian manifolds with upper bounds on the curvature (CAT(ϰ)-spaces), and establish similar result for normed spaces. acknowledgement: ' Supported by the Russian Foundation for Basic Research grant 18-01-00036.' article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Roman full_name: Karasev, Roman last_name: Karasev citation: ama: Akopyan A, Karasev R. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020;2020(3):669-697. doi:10.1093/imrn/rny037 apa: Akopyan, A., & Karasev, R. (2020). Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rny037 chicago: Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices. Oxford University Press, 2020. https://doi.org/10.1093/imrn/rny037. ieee: A. Akopyan and R. Karasev, “Waist of balls in hyperbolic and spherical spaces,” International Mathematics Research Notices, vol. 2020, no. 3. Oxford University Press, pp. 669–697, 2020. ista: Akopyan A, Karasev R. 2020. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020(3), 669–697. mla: Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices, vol. 2020, no. 3, Oxford University Press, 2020, pp. 669–97, doi:10.1093/imrn/rny037. short: A. Akopyan, R. Karasev, International Mathematics Research Notices 2020 (2020) 669–697. date_created: 2022-03-18T11:39:30Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-24T14:19:55Z day: '01' department: - _id: HeEd doi: 10.1093/imrn/rny037 external_id: arxiv: - '1702.07513' isi: - '000522852700002' intvolume: ' 2020' isi: 1 issue: '3' keyword: - General Mathematics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.07513 month: '02' oa: 1 oa_version: Preprint page: 669-697 publication: International Mathematics Research Notices publication_identifier: eissn: - 1687-0247 issn: - 1073-7928 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Waist of balls in hyperbolic and spherical spaces type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 2020 year: '2020' ... --- _id: '9799' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1 apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957469.v1 chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1. ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020. ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1. mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957469.v1. short: C. Fraisse, J.J. Welch, (2020). date_created: 2021-08-06T11:26:57Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '15' department: - _id: BeVi - _id: NiBa doi: 10.6084/m9.figshare.7957469.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7957469.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society of London related_material: record: - id: '6467' relation: used_in_publication status: public status: public title: Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9798' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1 apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957472.v1 chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1. ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020. ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1. mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957472.v1. short: C. Fraisse, J.J. Welch, (2020). date_created: 2021-08-06T11:18:15Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '15' department: - _id: BeVi - _id: NiBa doi: 10.6084/m9.figshare.7957472.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7957472.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society of London related_material: record: - id: '6467' relation: used_in_publication status: public status: public title: Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '6488' abstract: - lang: eng text: We prove a central limit theorem for the difference of linear eigenvalue statistics of a sample covariance matrix W˜ and its minor W. We find that the fluctuation of this difference is much smaller than those of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of W˜ and W. Our result identifies the fluctuation of the spatial derivative of the approximate Gaussian field in the recent paper by Dumitru and Paquette. Unlike in a similar result for Wigner matrices, for sample covariance matrices, the fluctuation may entirely vanish. article_number: '2050006' article_processing_charge: No article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: 'Cipolloni G, Erdös L. Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices. Random Matrices: Theory and Application. 2020;9(3). doi:10.1142/S2010326320500069' apa: 'Cipolloni, G., & Erdös, L. (2020). Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices. Random Matrices: Theory and Application. World Scientific Publishing. https://doi.org/10.1142/S2010326320500069' chicago: 'Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of Linear Eigenvalue Statistics for Sample Covariance Matrices.” Random Matrices: Theory and Application. World Scientific Publishing, 2020. https://doi.org/10.1142/S2010326320500069.' ieee: 'G. Cipolloni and L. Erdös, “Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices,” Random Matrices: Theory and Application, vol. 9, no. 3. World Scientific Publishing, 2020.' ista: 'Cipolloni G, Erdös L. 2020. Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices. Random Matrices: Theory and Application. 9(3), 2050006.' mla: 'Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of Linear Eigenvalue Statistics for Sample Covariance Matrices.” Random Matrices: Theory and Application, vol. 9, no. 3, 2050006, World Scientific Publishing, 2020, doi:10.1142/S2010326320500069.' short: 'G. Cipolloni, L. Erdös, Random Matrices: Theory and Application 9 (2020).' date_created: 2019-05-26T21:59:14Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-28T08:38:48Z day: '01' department: - _id: LaEr doi: 10.1142/S2010326320500069 ec_funded: 1 external_id: arxiv: - '1806.08751' isi: - '000547464400001' intvolume: ' 9' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.08751 month: '07' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: 'Random Matrices: Theory and Application' publication_identifier: eissn: - '20103271' issn: - '20103263' publication_status: published publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '8746' abstract: - lang: eng text: "Research in the field of colloidal semiconductor nanocrystals (NCs) has progressed tremendously, mostly because of their exceptional optoelectronic properties. Core@shell NCs, in which one or more inorganic layers overcoat individual NCs, recently received significant attention due to their remarkable optical characteristics. Reduced Auger recombination, suppressed blinking, and enhanced carrier multiplication are among the merits of core@shell NCs. Despite their importance in device development, the influence of the shell and the surface modification of the core@shell NC assemblies on the charge carrier transport remains a pertinent research objective. Type-II PbTe@PbS core@shell NCs, in which exclusive electron transport was demonstrated, still exhibit instability of their electron \r\n ransport. Here, we demonstrate the enhancement of electron transport and stability in PbTe@PbS core@shell NC assemblies using iodide as a surface passivating ligand. The combination of the PbS shelling and the use of the iodide ligand contributes to the addition of one mobile electron for each core@shell NC. Furthermore, both electron mobility and on/off current modulation ratio values of the core@shell NC field-effect transistor are steady with the usage of iodide. Excellent stability in these exclusively electron-transporting core@shell NCs paves the way for their utilization in electronic devices. " acknowledgement: "This work was partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No.\r\nJP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (No. SEED-18 16-2). We acknowledge Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility." article_number: '173101' article_processing_charge: No article_type: original author: - first_name: Retno full_name: Miranti, Retno last_name: Miranti - first_name: Ricky Dwi full_name: Septianto, Ricky Dwi last_name: Septianto - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Maksym V. full_name: Kovalenko, Maksym V. last_name: Kovalenko - first_name: Nobuhiro full_name: Matsushita, Nobuhiro last_name: Matsushita - first_name: Yoshihiro full_name: Iwasa, Yoshihiro last_name: Iwasa - first_name: Satria Zulkarnaen full_name: Bisri, Satria Zulkarnaen last_name: Bisri citation: ama: Miranti R, Septianto RD, Ibáñez M, et al. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 2020;117(17). doi:10.1063/5.0025965 apa: Miranti, R., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., Iwasa, Y., & Bisri, S. Z. (2020). Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0025965 chicago: Miranti, Retno, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” Applied Physics Letters. AIP Publishing, 2020. https://doi.org/10.1063/5.0025965. ieee: R. Miranti et al., “Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids,” Applied Physics Letters, vol. 117, no. 17. AIP Publishing, 2020. ista: Miranti R, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 117(17), 173101. mla: Miranti, Retno, et al. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” Applied Physics Letters, vol. 117, no. 17, 173101, AIP Publishing, 2020, doi:10.1063/5.0025965. short: R. Miranti, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, Applied Physics Letters 117 (2020). date_created: 2020-11-09T08:05:43Z date_published: 2020-10-26T00:00:00Z date_updated: 2023-09-05T11:57:23Z day: '26' department: - _id: MaIb doi: 10.1063/5.0025965 external_id: isi: - '000591639700001' intvolume: ' 117' isi: 1 issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1063/5.0025965 month: '10' oa: 1 oa_version: Published Version publication: Applied Physics Letters publication_identifier: eissn: - 1077-3118 issn: - 0003-6951 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 117 year: '2020' ... --- _id: '7985' abstract: - lang: eng text: The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells. acknowledgement: "S.A.F. is indebted to the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation programme (grant agreement No 636069)." article_processing_charge: No article_type: review author: - first_name: WJ full_name: Kwak, WJ last_name: Kwak - first_name: D full_name: Sharon, D last_name: Sharon - first_name: C full_name: Xia, C last_name: Xia - first_name: H full_name: Kim, H last_name: Kim - first_name: LR full_name: Johnson, LR last_name: Johnson - first_name: PG full_name: Bruce, PG last_name: Bruce - first_name: LF full_name: Nazar, LF last_name: Nazar - first_name: YK full_name: Sun, YK last_name: Sun - first_name: AA full_name: Frimer, AA last_name: Frimer - first_name: M full_name: Noked, M last_name: Noked - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: D full_name: Aurbach, D last_name: Aurbach citation: ama: 'Kwak W, Sharon D, Xia C, et al. Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. 2020;120(14):6626-6683. doi:10.1021/acs.chemrev.9b00609' apa: 'Kwak, W., Sharon, D., Xia, C., Kim, H., Johnson, L., Bruce, P., … Aurbach, D. (2020). Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.9b00609' chicago: 'Kwak, WJ, D Sharon, C Xia, H Kim, LR Johnson, PG Bruce, LF Nazar, et al. “Lithium-Oxygen Batteries and Related Systems: Potential, Status, and Future.” Chemical Reviews. American Chemical Society, 2020. https://doi.org/10.1021/acs.chemrev.9b00609.' ieee: 'W. Kwak et al., “Lithium-oxygen batteries and related systems: Potential, status, and future,” Chemical Reviews, vol. 120, no. 14. American Chemical Society, pp. 6626–6683, 2020.' ista: 'Kwak W, Sharon D, Xia C, Kim H, Johnson L, Bruce P, Nazar L, Sun Y, Frimer A, Noked M, Freunberger SA, Aurbach D. 2020. Lithium-oxygen batteries and related systems: Potential, status, and future. Chemical Reviews. 120(14), 6626–6683.' mla: 'Kwak, WJ, et al. “Lithium-Oxygen Batteries and Related Systems: Potential, Status, and Future.” Chemical Reviews, vol. 120, no. 14, American Chemical Society, 2020, pp. 6626–83, doi:10.1021/acs.chemrev.9b00609.' short: W. Kwak, D. Sharon, C. Xia, H. Kim, L. Johnson, P. Bruce, L. Nazar, Y. Sun, A. Frimer, M. Noked, S.A. Freunberger, D. Aurbach, Chemical Reviews 120 (2020) 6626–6683. date_created: 2020-06-19T08:42:47Z date_published: 2020-03-05T00:00:00Z date_updated: 2023-09-05T12:04:28Z day: '05' ddc: - '540' department: - _id: StFr doi: 10.1021/acs.chemrev.9b00609 external_id: isi: - '000555413600008' pmid: - '32134255' file: - access_level: open_access checksum: 1a683353d46c5841c8bb2ee0a56ac7be content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T16:36:01Z date_updated: 2020-07-14T12:48:06Z file_id: '8060' file_name: ChemRev_final.pdf file_size: 8525678 relation: main_file file_date_updated: 2020-07-14T12:48:06Z has_accepted_license: '1' intvolume: ' 120' isi: 1 issue: '14' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 6626-6683 pmid: 1 publication: Chemical Reviews publication_identifier: eissn: - 1520-6890 issn: - 0009-2665 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Lithium-oxygen batteries and related systems: Potential, status, and future' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 120 year: '2020' ... --- _id: '8721' abstract: - lang: eng text: Spontaneously arising channels that transport the phytohormone auxin provide positional cues for self-organizing aspects of plant development such as flexible vasculature regeneration or its patterning during leaf venation. The auxin canalization hypothesis proposes a feedback between auxin signaling and transport as the underlying mechanism, but molecular players await discovery. We identified part of the machinery that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like kinase) interact with and phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization, which macroscopically manifests as defects in leaf venation and vasculature regeneration after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback that coordinates polarization of individual cells during auxin canalization. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'We acknowledge M. Glanc and Y. Zhang for providing entryclones; Vienna Biocenter Core Facilities (VBCF) for recombinantprotein production and purification; Vienna Biocenter Massspectrometry Facility, Bioimaging, and Life Science Facilities at IST Austria and Proteomics Core Facility CEITEC for a great assistance.Funding:This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 742985) and Austrian Science Fund (FWF): I 3630-B25 to J.F.and by grants from the Austrian Academy of Science through the Gregor Mendel Institute (Y.B.) and the Austrian Agency for International Cooperation in Education and Research (D.D.); the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001) (W.S.); the Research Foundation–Flanders (FWO;Odysseus II G0D0515N) and a European Research Council grant (ERC; StG TORPEDO; 714055) to B.D.R., B.Y., and E.M.; and the Hertha Firnberg Programme postdoctoral fellowship (T-947) from the FWF Austrian Science Fund to E.S.-L.; J.H. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at IST Austria.' article_processing_charge: No article_type: original author: - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat - first_name: N full_name: Rydza, N last_name: Rydza - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: David full_name: Domjan, David id: C684CD7A-257E-11EA-9B6F-D8588B4F947F last_name: Domjan orcid: 0000-0003-2267-106X - first_name: E full_name: Mazur, E last_name: Mazur - first_name: E full_name: Smakowska-Luzan, E last_name: Smakowska-Luzan - first_name: W full_name: Smet, W last_name: Smet - first_name: E full_name: Mor, E last_name: Mor - first_name: J full_name: Nolf, J last_name: Nolf - first_name: B full_name: Yang, B last_name: Yang - first_name: W full_name: Grunewald, W last_name: Grunewald - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Y full_name: Belkhadir, Y last_name: Belkhadir - first_name: B full_name: De Rybel, B last_name: De Rybel - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Hajny J, Prat T, Rydza N, et al. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. 2020;370(6516):550-557. doi:10.1126/science.aba3178 apa: Hajny, J., Prat, T., Rydza, N., Rodriguez Solovey, L., Tan, S., Verstraeten, I., … Friml, J. (2020). Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba3178 chicago: Hajny, Jakub, Tomas Prat, N Rydza, Lesia Rodriguez Solovey, Shutang Tan, Inge Verstraeten, David Domjan, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba3178. ieee: J. Hajny et al., “Receptor kinase module targets PIN-dependent auxin transport during canalization,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, pp. 550–557, 2020. ista: Hajny J, Prat T, Rydza N, Rodriguez Solovey L, Tan S, Verstraeten I, Domjan D, Mazur E, Smakowska-Luzan E, Smet W, Mor E, Nolf J, Yang B, Grunewald W, Molnar G, Belkhadir Y, De Rybel B, Friml J. 2020. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. 370(6516), 550–557. mla: Hajny, Jakub, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” Science, vol. 370, no. 6516, American Association for the Advancement of Science, 2020, pp. 550–57, doi:10.1126/science.aba3178. short: J. Hajny, T. Prat, N. Rydza, L. Rodriguez Solovey, S. Tan, I. Verstraeten, D. Domjan, E. Mazur, E. Smakowska-Luzan, W. Smet, E. Mor, J. Nolf, B. Yang, W. Grunewald, G. Molnar, Y. Belkhadir, B. De Rybel, J. Friml, Science 370 (2020) 550–557. date_created: 2020-11-02T10:04:46Z date_published: 2020-10-30T00:00:00Z date_updated: 2023-09-05T12:02:35Z day: '30' department: - _id: JiFr doi: 10.1126/science.aba3178 ec_funded: 1 external_id: isi: - '000583031800041' pmid: - '33122378' intvolume: ' 370' isi: 1 issue: '6516' language: - iso: eng main_file_link: - open_access: '1' url: https://europepmc.org/article/MED/33122378#free-full-text month: '10' oa: 1 oa_version: Published Version page: 550-557 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 2699E3D2-B435-11E9-9278-68D0E5697425 grant_number: '25239' name: Cell surface receptor complexes for PIN polarity and auxin-mediated development publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/molecular-compass-for-cell-orientation/ scopus_import: '1' status: public title: Receptor kinase module targets PIN-dependent auxin transport during canalization type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 370 year: '2020' ... --- _id: '7968' abstract: - lang: eng text: Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Yossi full_name: Paltiel, Yossi last_name: Paltiel - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Ghazaryan A, Paltiel Y, Lemeshko M. Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. 2020;124(21):11716-11721. doi:10.1021/acs.jpcc.0c02584 apa: Ghazaryan, A., Paltiel, Y., & Lemeshko, M. (2020). Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/acs.jpcc.0c02584 chicago: Ghazaryan, Areg, Yossi Paltiel, and Mikhail Lemeshko. “Analytic Model of Chiral-Induced Spin Selectivity.” The Journal of Physical Chemistry C. American Chemical Society, 2020. https://doi.org/10.1021/acs.jpcc.0c02584. ieee: A. Ghazaryan, Y. Paltiel, and M. Lemeshko, “Analytic model of chiral-induced spin selectivity,” The Journal of Physical Chemistry C, vol. 124, no. 21. American Chemical Society, pp. 11716–11721, 2020. ista: Ghazaryan A, Paltiel Y, Lemeshko M. 2020. Analytic model of chiral-induced spin selectivity. The Journal of Physical Chemistry C. 124(21), 11716–11721. mla: Ghazaryan, Areg, et al. “Analytic Model of Chiral-Induced Spin Selectivity.” The Journal of Physical Chemistry C, vol. 124, no. 21, American Chemical Society, 2020, pp. 11716–21, doi:10.1021/acs.jpcc.0c02584. short: A. Ghazaryan, Y. Paltiel, M. Lemeshko, The Journal of Physical Chemistry C 124 (2020) 11716–11721. date_created: 2020-06-16T14:29:59Z date_published: 2020-05-04T00:00:00Z date_updated: 2023-09-05T12:07:15Z day: '04' ddc: - '530' department: - _id: MiLe doi: 10.1021/acs.jpcc.0c02584 ec_funded: 1 external_id: isi: - '000614616200006' file: - access_level: open_access checksum: 25932bb1d0b0a955be0bea4d17facd49 content_type: application/pdf creator: kschuh date_created: 2020-10-20T14:39:47Z date_updated: 2020-10-20T14:39:47Z file_id: '8683' file_name: 2020_PhysChemC_Ghazaryan.pdf file_size: 1543429 relation: main_file success: 1 file_date_updated: 2020-10-20T14:39:47Z has_accepted_license: '1' intvolume: ' 124' isi: 1 issue: '21' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '05' oa: 1 oa_version: Published Version page: 11716-11721 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: The Journal of Physical Chemistry C publication_identifier: eissn: - 1932-7455 issn: - 1932-7447 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Analytic model of chiral-induced spin selectivity 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 124 year: '2020' ... --- _id: '10866' abstract: - lang: eng text: Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management. acknowledgement: "J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA." article_processing_charge: No article_type: original author: - first_name: Jiahua full_name: Duan, Jiahua last_name: Duan - first_name: Nathaniel full_name: Capote-Robayna, Nathaniel last_name: Capote-Robayna - first_name: Javier full_name: Taboada-Gutiérrez, Javier last_name: Taboada-Gutiérrez - first_name: Gonzalo full_name: Álvarez-Pérez, Gonzalo last_name: Álvarez-Pérez - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: Javier full_name: Martín-Sánchez, Javier last_name: Martín-Sánchez - first_name: Alexey Y. full_name: Nikitin, Alexey Y. last_name: Nikitin - first_name: Pablo full_name: Alonso-González, Pablo last_name: Alonso-González citation: ama: 'Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 2020;20(7):5323-5329. doi:10.1021/acs.nanolett.0c01673' apa: 'Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01673' chicago: 'Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01673.' ieee: 'J. Duan et al., “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020.' ista: 'Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.' mla: 'Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:10.1021/acs.nanolett.0c01673.' short: J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329. date_created: 2022-03-18T11:37:38Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-09-05T12:05:58Z day: '01' department: - _id: NanoFab doi: 10.1021/acs.nanolett.0c01673 external_id: arxiv: - '2004.14599' isi: - '000548893200082' pmid: - '32530634' intvolume: ' 20' isi: 1 issue: '7' keyword: - Mechanical Engineering - Condensed Matter Physics - General Materials Science - General Chemistry - Bioengineering language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2004.14599 month: '07' oa: 1 oa_version: Preprint page: 5323-5329 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 20 year: '2020' ... --- _id: '8588' abstract: - lang: eng text: Dipolar (or spatially indirect) excitons (IXs) in semiconductor double quantum well (DQW) subjected to an electric field are neutral species with a dipole moment oriented perpendicular to the DQW plane. Here, we theoretically study interactions between IXs in stacked DQW bilayers, where the dipolar coupling can be either attractive or repulsive depending on the relative positions of the particles. By using microscopic band structure calculations to determine the electronic states forming the excitons, we show that the attractive dipolar interaction between stacked IXs deforms their electronic wave function, thereby increasing the inter-DQW interaction energy and making the IX even more electrically polarizable. Many-particle interaction effects are addressed by considering the coupling between a single IX in one of the DQWs to a cloud of IXs in the other DQW, which is modeled either as a closed-packed lattice or as a continuum IX fluid. We find that the lattice model yields IX interlayer binding energies decreasing with increasing lattice density. This behavior is due to the dominating role of the intra-DQW dipolar repulsion, which prevents more than one exciton from entering the attractive region of the inter-DQW coupling. Finally, both models shows that the single IX distorts the distribution of IXs in the adjacent DQW, thus inducing the formation of an IX dipolar polaron (dipolaron). While the interlayer binding energy reduces with IX density for lattice dipolarons, the continuous polaron model predicts a nonmonotonous dependence on density in semiquantitative agreement with a recent experimental study [cf. Hubert et al., Phys. Rev. X 9, 021026 (2019)]. acknowledgement: "We thank W. Kaganer for discussions and for comment on the manuscript. We acknowledge the financial support from the German-Israeli Foundation (GIF), grant agreement I-1277-303.10/2014. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation\r\nprogram under the Marie Skodowska-Curie grant agreement No 754411. P.V.S acknowledges financial support\r\nfrom the Deutsche Forschungsgemeinschaft (DFG) under\r\nProject No. SA 598/12-1." article_number: '045307' article_processing_charge: No article_type: original author: - first_name: C. full_name: Hubert, C. last_name: Hubert - first_name: K. full_name: Cohen, K. last_name: Cohen - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: R. full_name: Rapaport, R. last_name: Rapaport - first_name: P. V. full_name: Santos, P. V. last_name: Santos citation: ama: Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 2020;102(4). doi:10.1103/physrevb.102.045307 apa: Hubert, C., Cohen, K., Ghazaryan, A., Lemeshko, M., Rapaport, R., & Santos, P. V. (2020). Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.045307 chicago: Hubert, C., K. Cohen, Areg Ghazaryan, Mikhail Lemeshko, R. Rapaport, and P. V. Santos. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.045307. ieee: C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, and P. V. Santos, “Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids,” Physical Review B, vol. 102, no. 4. American Physical Society, 2020. ista: Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. 2020. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 102(4), 045307. mla: Hubert, C., et al. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” Physical Review B, vol. 102, no. 4, 045307, American Physical Society, 2020, doi:10.1103/physrevb.102.045307. short: C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, P.V. Santos, Physical Review B 102 (2020). date_created: 2020-09-30T10:33:43Z date_published: 2020-07-21T00:00:00Z date_updated: 2023-09-05T12:12:10Z day: '21' department: - _id: MiLe doi: 10.1103/physrevb.102.045307 ec_funded: 1 external_id: arxiv: - '1910.06015' isi: - '000550579100004' intvolume: ' 102' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.06015 month: '07' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 102 year: '2020' ... --- _id: '8769' abstract: - lang: eng text: One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas. acknowledgement: "We are grateful to M. Correggi, A. Deuchert, and P. Schmelcher for valuable discussions. We also thank the anonymous referees for helping to clarify a few important points in the experimental realization. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement\r\nNo 754411. D.L. acknowledges financial support from the Goran Gustafsson Foundation (grant no. 1804) and LMU Munich. R.S., M.L., and N.R. gratefully acknowledge financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 694227, No 801770, and No 758620, respectively)." article_number: '144109' article_processing_charge: No article_type: original author: - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: D. full_name: Lundholm, D. last_name: Lundholm - first_name: N. full_name: Rougerie, N. last_name: Rougerie - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. Quantum impurity model for anyons. Physical Review B. 2020;102(14). doi:10.1103/physrevb.102.144109 apa: Yakaboylu, E., Ghazaryan, A., Lundholm, D., Rougerie, N., Lemeshko, M., & Seiringer, R. (2020). Quantum impurity model for anyons. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.144109 chicago: Yakaboylu, Enderalp, Areg Ghazaryan, D. Lundholm, N. Rougerie, Mikhail Lemeshko, and Robert Seiringer. “Quantum Impurity Model for Anyons.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.144109. ieee: E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, and R. Seiringer, “Quantum impurity model for anyons,” Physical Review B, vol. 102, no. 14. American Physical Society, 2020. ista: Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. 2020. Quantum impurity model for anyons. Physical Review B. 102(14), 144109. mla: Yakaboylu, Enderalp, et al. “Quantum Impurity Model for Anyons.” Physical Review B, vol. 102, no. 14, 144109, American Physical Society, 2020, doi:10.1103/physrevb.102.144109. short: E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, R. Seiringer, Physical Review B 102 (2020). date_created: 2020-11-18T07:34:17Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-09-05T12:12:30Z day: '01' department: - _id: MiLe - _id: RoSe doi: 10.1103/physrevb.102.144109 ec_funded: 1 external_id: arxiv: - '1912.07890' isi: - '000582563300001' intvolume: ' 102' isi: 1 issue: '14' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.07890 month: '10' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Quantum impurity model for anyons type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 102 year: '2020' ... --- _id: '7971' abstract: - lang: eng text: Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state. article_number: '245411' article_processing_charge: No article_type: original author: - first_name: Peng full_name: Rao, Peng id: 47C23AC6-02D0-11E9-BD0E-99399A5D3DEB last_name: Rao orcid: 0000-0003-1250-0021 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Rao P, Serbyn M. Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. 2020;101(24). doi:10.1103/physrevb.101.245411 apa: Rao, P., & Serbyn, M. (2020). Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.101.245411 chicago: Rao, Peng, and Maksym Serbyn. “Gully Quantum Hall Ferromagnetism in Biased Trilayer Graphene.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.101.245411. ieee: P. Rao and M. Serbyn, “Gully quantum Hall ferromagnetism in biased trilayer graphene,” Physical Review B, vol. 101, no. 24. American Physical Society, 2020. ista: Rao P, Serbyn M. 2020. Gully quantum Hall ferromagnetism in biased trilayer graphene. Physical Review B. 101(24), 245411. mla: Rao, Peng, and Maksym Serbyn. “Gully Quantum Hall Ferromagnetism in Biased Trilayer Graphene.” Physical Review B, vol. 101, no. 24, 245411, American Physical Society, 2020, doi:10.1103/physrevb.101.245411. short: P. Rao, M. Serbyn, Physical Review B 101 (2020). date_created: 2020-06-17T14:52:06Z date_published: 2020-06-15T00:00:00Z date_updated: 2023-09-05T12:11:37Z day: '15' department: - _id: MaSe doi: 10.1103/physrevb.101.245411 external_id: isi: - '000538715500010' intvolume: ' 101' isi: 1 issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.05739 month: '06' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Gully quantum Hall ferromagnetism in biased trilayer graphene type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 101 year: '2020' ... --- _id: '8634' abstract: - lang: eng text: In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent. acknowledgement: M. F. S. and R. O. G. acknowledge funding from the National Science Foundation (CMMI-1234436, DMS1125302, CMMI-1725587) and Defense Advanced Research Projects Agency (HR0011-16-2-0033). B. S.has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013/ under REA Grant Agreement No. 291734. article_number: '064501' article_processing_charge: No article_type: original author: - first_name: Balachandra full_name: Suri, Balachandra id: 47A5E706-F248-11E8-B48F-1D18A9856A87 last_name: Suri - first_name: Logan full_name: Kageorge, Logan last_name: Kageorge - first_name: Roman O. full_name: Grigoriev, Roman O. last_name: Grigoriev - first_name: Michael F. full_name: Schatz, Michael F. last_name: Schatz citation: ama: Suri B, Kageorge L, Grigoriev RO, Schatz MF. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 2020;125(6). doi:10.1103/physrevlett.125.064501 apa: Suri, B., Kageorge, L., Grigoriev, R. O., & Schatz, M. F. (2020). Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.064501 chicago: Suri, Balachandra, Logan Kageorge, Roman O. Grigoriev, and Michael F. Schatz. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.064501. ieee: B. Suri, L. Kageorge, R. O. Grigoriev, and M. F. Schatz, “Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits,” Physical Review Letters, vol. 125, no. 6. American Physical Society, 2020. ista: Suri B, Kageorge L, Grigoriev RO, Schatz MF. 2020. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 125(6), 064501. mla: Suri, Balachandra, et al. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters, vol. 125, no. 6, 064501, American Physical Society, 2020, doi:10.1103/physrevlett.125.064501. short: B. Suri, L. Kageorge, R.O. Grigoriev, M.F. Schatz, Physical Review Letters 125 (2020). date_created: 2020-10-08T17:27:32Z date_published: 2020-08-05T00:00:00Z date_updated: 2023-09-05T12:08:29Z day: '05' department: - _id: BjHo doi: 10.1103/physrevlett.125.064501 ec_funded: 1 external_id: arxiv: - '2008.02367' isi: - '000555785600005' intvolume: ' 125' isi: 1 issue: '6' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.02367 month: '08' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme 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: Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 125 year: '2020' ... --- _id: '7949' abstract: - lang: eng text: Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-terminally encoded peptide 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance. acknowledgement: We thank Maria Njo, Sarah De Cokere, Marieke Mispelaere and Darren Wells, for practical assistance, Daniël Van Damme for assistance with image analysis, Marnik Vuylsteke for advice on statistics, Catherine Perrot-Rechenmann for useful discussions, Steffen Lau for critical reading oft he manuscript, and Philip Benfey, Gerd Jürgens, Philippe Nacry, Frederik Börnke, and Frans Tax for sharing materials. article_processing_charge: No article_type: original author: - first_name: S full_name: Smith, S last_name: Smith - first_name: S full_name: Zhu, S last_name: Zhu - first_name: L full_name: Joos, L last_name: Joos - first_name: I full_name: Roberts, I last_name: Roberts - first_name: N full_name: Nikonorova, N last_name: Nikonorova - first_name: LD full_name: Vu, LD last_name: Vu - first_name: E full_name: Stes, E last_name: Stes - first_name: H full_name: Cho, H last_name: Cho - first_name: A full_name: Larrieu, A last_name: Larrieu - first_name: W full_name: Xuan, W last_name: Xuan - first_name: B full_name: Goodall, B last_name: Goodall - first_name: B full_name: van de Cotte, B last_name: van de Cotte - first_name: JM full_name: Waite, JM last_name: Waite - first_name: A full_name: Rigal, A last_name: Rigal - first_name: SR full_name: R Harborough, SR last_name: R Harborough - first_name: G full_name: Persiau, G last_name: Persiau - first_name: S full_name: Vanneste, S last_name: Vanneste - first_name: GK full_name: Kirschner, GK last_name: Kirschner - first_name: E full_name: Vandermarliere, E last_name: Vandermarliere - first_name: L full_name: Martens, L last_name: Martens - first_name: Y full_name: Stahl, Y last_name: Stahl - first_name: D full_name: Audenaert, D last_name: Audenaert - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: G full_name: Felix, G last_name: Felix - first_name: R full_name: Simon, R last_name: Simon - first_name: M full_name: Bennett, M last_name: Bennett - first_name: A full_name: Bishopp, A last_name: Bishopp - first_name: G full_name: De Jaeger, G last_name: De Jaeger - first_name: K full_name: Ljung, K last_name: Ljung - first_name: S full_name: Kepinski, S last_name: Kepinski - first_name: S full_name: Robert, S last_name: Robert - first_name: J full_name: Nemhauser, J last_name: Nemhauser - first_name: I full_name: Hwang, I last_name: Hwang - first_name: K full_name: Gevaert, K last_name: Gevaert - first_name: T full_name: Beeckman, T last_name: Beeckman - first_name: I full_name: De Smet, I last_name: De Smet citation: ama: Smith S, Zhu S, Joos L, et al. The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. 2020;19(8):1248-1262. doi:10.1074/mcp.ra119.001826 apa: Smith, S., Zhu, S., Joos, L., Roberts, I., Nikonorova, N., Vu, L., … De Smet, I. (2020). The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/mcp.ra119.001826 chicago: Smith, S, S Zhu, L Joos, I Roberts, N Nikonorova, LD Vu, E Stes, et al. “The CEP5 Peptide Promotes Abiotic Stress Tolerance, as Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis.” Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology, 2020. https://doi.org/10.1074/mcp.ra119.001826. ieee: S. Smith et al., “The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis,” Molecular & Cellular Proteomics, vol. 19, no. 8. American Society for Biochemistry and Molecular Biology, pp. 1248–1262, 2020. ista: Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu L, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite J, Rigal A, R Harborough S, Persiau G, Vanneste S, Kirschner G, Vandermarliere E, Martens L, Stahl Y, Audenaert D, Friml J, Felix G, Simon R, Bennett M, Bishopp A, De Jaeger G, Ljung K, Kepinski S, Robert S, Nemhauser J, Hwang I, Gevaert K, Beeckman T, De Smet I. 2020. The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Molecular & Cellular Proteomics. 19(8), 1248–1262. mla: Smith, S., et al. “The CEP5 Peptide Promotes Abiotic Stress Tolerance, as Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis.” Molecular & Cellular Proteomics, vol. 19, no. 8, American Society for Biochemistry and Molecular Biology, 2020, pp. 1248–62, doi:10.1074/mcp.ra119.001826. short: S. Smith, S. Zhu, L. Joos, I. Roberts, N. Nikonorova, L. Vu, E. Stes, H. Cho, A. Larrieu, W. Xuan, B. Goodall, B. van de Cotte, J. Waite, A. Rigal, S. R Harborough, G. Persiau, S. Vanneste, G. Kirschner, E. Vandermarliere, L. Martens, Y. Stahl, D. Audenaert, J. Friml, G. Felix, R. Simon, M. Bennett, A. Bishopp, G. De Jaeger, K. Ljung, S. Kepinski, S. Robert, J. Nemhauser, I. Hwang, K. Gevaert, T. Beeckman, I. De Smet, Molecular & Cellular Proteomics 19 (2020) 1248–1262. date_created: 2020-06-08T10:10:53Z date_published: 2020-08-01T00:00:00Z date_updated: 2023-09-05T12:17:46Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1074/mcp.ra119.001826 external_id: isi: - '000561114000001' pmid: - '32404488' file: - access_level: open_access checksum: 3f3f37b4a1ba2cfd270fc7733dd89680 content_type: application/pdf creator: kschuh date_created: 2021-05-05T10:10:14Z date_updated: 2021-05-05T10:10:14Z file_id: '9373' file_name: 2020_MCP_Smith.pdf file_size: 1632311 relation: main_file success: 1 file_date_updated: 2021-05-05T10:10:14Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 1248-1262 pmid: 1 publication: Molecular & Cellular Proteomics publication_identifier: eissn: - 1535-9484 publication_status: published publisher: American Society for Biochemistry and Molecular Biology quality_controlled: '1' scopus_import: '1' status: public title: The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2020' ... --- _id: '7619' abstract: - lang: eng text: Cell polarity is a fundamental feature of all multicellular organisms. In plants, prominent cell polarity markers are PIN auxin transporters crucial for plant development. To identify novel components involved in cell polarity establishment and maintenance, we carried out a forward genetic screening with PIN2:PIN1-HA;pin2 Arabidopsis plants, which ectopically express predominantly basally localized PIN1 in the root epidermal cells leading to agravitropic root growth. From the screen, we identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused PIN1-HA polarity switch from basal to apical side of root epidermal cells. Complementation experiments established the repp12 causative mutation as an amino acid substitution in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase with predicted function in vesicle formation. ala3 T-DNA mutants show defects in many auxin-regulated processes, in asymmetric auxin distribution and in PIN trafficking. Analysis of quintuple and sextuple mutants confirmed a crucial role of ALA proteins in regulating plant development and in PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with GNOM and BIG3 ARF GEFs. Taken together, our results identified ALA3 flippase as an important interactor and regulator of ARF GEF functioning in PIN polarity, trafficking and auxin-mediated development. acknowledged_ssus: - _id: Bio article_processing_charge: No article_type: original author: - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Petra full_name: Marhavá, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Marhavá - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Vendula full_name: Pukyšová, Vendula last_name: Pukyšová - first_name: Adrià Sans full_name: Sánchez, Adrià Sans last_name: Sánchez - first_name: Vivek Kumar full_name: Raxwal, Vivek Kumar last_name: Raxwal - first_name: Christian S. full_name: Hardtke, Christian S. last_name: Hardtke - first_name: Tomasz full_name: Nodzynski, Tomasz last_name: Nodzynski - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang X, Adamowski M, Marhavá P, et al. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 2020;32(5):1644-1664. doi:10.1105/tpc.19.00869 apa: Zhang, X., Adamowski, M., Marhavá, P., Tan, S., Zhang, Y., Rodriguez Solovey, L., … Friml, J. (2020). Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.19.00869 chicago: Zhang, Xixi, Maciek Adamowski, Petra Marhavá, Shutang Tan, Yuzhou Zhang, Lesia Rodriguez Solovey, Marta Zwiewka, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” The Plant Cell. American Society of Plant Biologists, 2020. https://doi.org/10.1105/tpc.19.00869. ieee: X. Zhang et al., “Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters,” The Plant Cell, vol. 32, no. 5. American Society of Plant Biologists, pp. 1644–1664, 2020. ista: Zhang X, Adamowski M, Marhavá P, Tan S, Zhang Y, Rodriguez Solovey L, Zwiewka M, Pukyšová V, Sánchez AS, Raxwal VK, Hardtke CS, Nodzynski T, Friml J. 2020. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 32(5), 1644–1664. mla: Zhang, Xixi, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” The Plant Cell, vol. 32, no. 5, American Society of Plant Biologists, 2020, pp. 1644–64, doi:10.1105/tpc.19.00869. short: X. Zhang, M. Adamowski, P. Marhavá, S. Tan, Y. Zhang, L. Rodriguez Solovey, M. Zwiewka, V. Pukyšová, A.S. Sánchez, V.K. Raxwal, C.S. Hardtke, T. Nodzynski, J. Friml, The Plant Cell 32 (2020) 1644–1664. date_created: 2020-03-28T07:39:22Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-09-05T12:21:06Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.19.00869 ec_funded: 1 external_id: isi: - '000545741500030' pmid: - '32193204' intvolume: ' 32' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1105/tpc.19.00869 month: '05' oa: 1 oa_version: Published Version page: 1644-1664 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: The Plant Cell publication_identifier: eissn: - 1532-298X issn: - 1040-4651 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' scopus_import: '1' status: public title: Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2020' ... --- _id: '8607' abstract: - lang: eng text: Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants. article_processing_charge: No article_type: original author: - first_name: D full_name: Liu, D last_name: Liu - first_name: R full_name: Kumar, R last_name: Kumar - first_name: Claus full_name: LAN, Claus last_name: LAN - 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: W full_name: Siao, W last_name: Siao - first_name: I full_name: Vanhoutte, I last_name: Vanhoutte - first_name: P full_name: Wang, P last_name: Wang - first_name: KW full_name: Bender, KW last_name: Bender - first_name: K full_name: Yperman, K last_name: Yperman - first_name: S full_name: Martins, S last_name: Martins - first_name: X full_name: Zhao, X last_name: Zhao - first_name: G full_name: Vert, G last_name: Vert - first_name: D full_name: Van Damme, D last_name: Van Damme - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: E full_name: Russinova, E last_name: Russinova citation: ama: Liu D, Kumar R, LAN C, et al. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 2020;32(11):3598-3612. doi:10.1105/tpc.20.00384 apa: Liu, D., Kumar, R., LAN, C., Johnson, A. J., Siao, W., Vanhoutte, I., … Russinova, E. (2020). Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.20.00384 chicago: Liu, D, R Kumar, Claus LAN, Alexander J Johnson, W Siao, I Vanhoutte, P Wang, et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell. American Society of Plant Biologists, 2020. https://doi.org/10.1105/tpc.20.00384. ieee: D. Liu et al., “Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif,” Plant Cell, vol. 32, no. 11. American Society of Plant Biologists, pp. 3598–3612, 2020. ista: Liu D, Kumar R, LAN C, Johnson AJ, Siao W, Vanhoutte I, Wang P, Bender K, Yperman K, Martins S, Zhao X, Vert G, Van Damme D, Friml J, Russinova E. 2020. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 32(11), 3598–3612. mla: Liu, D., et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell, vol. 32, no. 11, American Society of Plant Biologists, 2020, pp. 3598–612, doi:10.1105/tpc.20.00384. short: D. Liu, R. Kumar, C. LAN, A.J. Johnson, W. Siao, I. Vanhoutte, P. Wang, K. Bender, K. Yperman, S. Martins, X. Zhao, G. Vert, D. Van Damme, J. Friml, E. Russinova, Plant Cell 32 (2020) 3598–3612. date_created: 2020-10-05T12:45:16Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-09-05T12:21:32Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.20.00384 ec_funded: 1 external_id: isi: - '000600226800021' pmid: - '32958564' intvolume: ' 32' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://europepmc.org/article/MED/32958564 month: '11' oa: 1 oa_version: Published Version page: 3598-3612 pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Plant Cell publication_identifier: eissn: - 1532-298x issn: - 1040-4651 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' scopus_import: '1' status: public title: Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2020' ... --- _id: '7695' abstract: - lang: eng text: The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex. article_processing_charge: No article_type: original author: - first_name: J full_name: Wang, J last_name: Wang - first_name: E full_name: Mylle, E last_name: Mylle - 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: N full_name: Besbrugge, N last_name: Besbrugge - first_name: G full_name: De Jaeger, G last_name: De Jaeger - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: R full_name: Pleskot, R last_name: Pleskot - first_name: D full_name: van Damme, D last_name: van Damme citation: ama: Wang J, Mylle E, Johnson AJ, et al. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 2020;183(3):986-997. doi:10.1104/pp.20.00178 apa: Wang, J., Mylle, E., Johnson, A. J., Besbrugge, N., De Jaeger, G., Friml, J., … van Damme, D. (2020). High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00178 chicago: Wang, J, E Mylle, Alexander J Johnson, N Besbrugge, G De Jaeger, Jiří Friml, R Pleskot, and D van Damme. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00178. ieee: J. Wang et al., “High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits,” Plant Physiology, vol. 183, no. 3. American Society of Plant Biologists, pp. 986–997, 2020. ista: Wang J, Mylle E, Johnson AJ, Besbrugge N, De Jaeger G, Friml J, Pleskot R, van Damme D. 2020. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 183(3), 986–997. mla: Wang, J., et al. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” Plant Physiology, vol. 183, no. 3, American Society of Plant Biologists, 2020, pp. 986–97, doi:10.1104/pp.20.00178. short: J. Wang, E. Mylle, A.J. Johnson, N. Besbrugge, G. De Jaeger, J. Friml, R. Pleskot, D. van Damme, Plant Physiology 183 (2020) 986–997. date_created: 2020-04-29T15:23:00Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-09-05T12:20:02Z day: '01' department: - _id: JiFr doi: 10.1104/pp.20.00178 external_id: isi: - '000550682000018' pmid: - '32321842' intvolume: ' 183' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.02.13.948109 month: '07' oa: 1 oa_version: Preprint page: 986-997 pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' scopus_import: '1' status: public title: High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 183 year: '2020' ... --- _id: '9197' abstract: - lang: eng text: In this paper we introduce and study all-pay bidding games, a class of two player, zero-sum games on graphs. The game proceeds as follows. We place a token on some vertex in the graph and assign budgets to the two players. Each turn, each player submits a sealed legal bid (non-negative and below their remaining budget), which is deducted from their budget and the highest bidder moves the token onto an adjacent vertex. The game ends once a sink is reached, and Player 1 pays Player 2 the outcome that is associated with the sink. The players attempt to maximize their expected outcome. Our games model settings where effort (of no inherent value) needs to be invested in an ongoing and stateful manner. On the negative side, we show that even in simple games on DAGs, optimal strategies may require a distribution over bids with infinite support. A central quantity in bidding games is the ratio of the players budgets. On the positive side, we show a simple FPTAS for DAGs, that, for each budget ratio, outputs an approximation for the optimal strategy for that ratio. We also implement it, show that it performs well, and suggests interesting properties of these games. Then, given an outcome c, we show an algorithm for finding the necessary and sufficient initial ratio for guaranteeing outcome c with probability 1 and a strategy ensuring such. Finally, while the general case has not previously been studied, solving the specific game in which Player 1 wins iff he wins the first two auctions, has been long stated as an open question, which we solve. acknowledgement: This research was supported by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship). article_processing_charge: No article_type: original author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 citation: ama: Avni G, Ibsen-Jensen R, Tkadlec J. All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. 2020;34(02):1798-1805. doi:10.1609/aaai.v34i02.5546 apa: 'Avni, G., Ibsen-Jensen, R., & Tkadlec, J. (2020). All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i02.5546' chicago: Avni, Guy, Rasmus Ibsen-Jensen, and Josef Tkadlec. “All-Pay Bidding Games on Graphs.” Proceedings of the AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i02.5546. ieee: G. Avni, R. Ibsen-Jensen, and J. Tkadlec, “All-pay bidding games on graphs,” Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, no. 02. Association for the Advancement of Artificial Intelligence, pp. 1798–1805, 2020. ista: Avni G, Ibsen-Jensen R, Tkadlec J. 2020. All-pay bidding games on graphs. Proceedings of the AAAI Conference on Artificial Intelligence. 34(02), 1798–1805. mla: Avni, Guy, et al. “All-Pay Bidding Games on Graphs.” Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, no. 02, Association for the Advancement of Artificial Intelligence, 2020, pp. 1798–805, doi:10.1609/aaai.v34i02.5546. short: G. Avni, R. Ibsen-Jensen, J. Tkadlec, Proceedings of the AAAI Conference on Artificial Intelligence 34 (2020) 1798–1805. conference: end_date: 2020-02-12 location: New York, NY, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2020-02-07 date_created: 2021-02-25T09:05:18Z date_published: 2020-04-03T00:00:00Z date_updated: 2023-09-05T12:40:00Z day: '03' department: - _id: ToHe - _id: KrCh doi: 10.1609/aaai.v34i02.5546 external_id: arxiv: - '1911.08360' intvolume: ' 34' issue: '02' language: - iso: eng month: '04' oa_version: Preprint page: 1798-1805 project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory publication: Proceedings of the AAAI Conference on Artificial Intelligence publication_identifier: eissn: - 2374-3468 isbn: - '9781577358350' issn: - 2159-5399 publication_status: published publisher: Association for the Advancement of Artificial Intelligence quality_controlled: '1' scopus_import: '1' status: public title: All-pay bidding games on graphs type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 34 year: '2020' ... --- _id: '8142' abstract: - lang: eng text: Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship (ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738 to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B. article_number: e104238 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: A full_name: Abuzeineh, A last_name: Abuzeineh - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Alba full_name: Juanes Garcia, Alba id: 40F05888-F248-11E8-B48F-1D18A9856A87 last_name: Juanes Garcia orcid: 0000-0002-1009-9652 - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: J full_name: Petrášek, J last_name: Petrášek - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 2020;39(17). doi:10.15252/embj.2019104238 apa: Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös, K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. Embo Press. https://doi.org/10.15252/embj.2019104238 chicago: Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia, Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal. Embo Press, 2020. https://doi.org/10.15252/embj.2019104238. ieee: J. C. Montesinos López et al., “Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage,” The Embo Journal, vol. 39, no. 17. Embo Press, 2020. ista: Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 39(17), e104238. mla: Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal, vol. 39, no. 17, e104238, Embo Press, 2020, doi:10.15252/embj.2019104238. short: J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös, J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020). date_created: 2020-07-21T09:08:38Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-05T13:05:47Z day: '01' ddc: - '580' department: - _id: MiSi - _id: EvBe doi: 10.15252/embj.2019104238 external_id: isi: - '000548311800001' pmid: - '32667089' file: - access_level: open_access checksum: 43d2b36598708e6ab05c69074e191d57 content_type: application/pdf creator: dernst date_created: 2020-12-02T09:13:23Z date_updated: 2020-12-02T09:13:23Z file_id: '8827' file_name: 2020_EMBO_Montesinos.pdf file_size: 3497156 relation: main_file success: 1 file_date_updated: 2020-12-02T09:13:23Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '17' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 253E54C8-B435-11E9-9278-68D0E5697425 grant_number: ALTF710-2016 name: Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development publication: The Embo Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 39 year: '2020' ... --- _id: '8084' abstract: - lang: eng text: Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation. article_processing_charge: No article_type: original author: - first_name: Fabrizio full_name: Lombardi, Fabrizio id: A057D288-3E88-11E9-986D-0CF4E5697425 last_name: Lombardi orcid: 0000-0003-2623-5249 - first_name: Manuel full_name: Gómez-Extremera, Manuel last_name: Gómez-Extremera - first_name: Pedro full_name: Bernaola-Galván, Pedro last_name: Bernaola-Galván - first_name: Ramalingam full_name: Vetrivelan, Ramalingam last_name: Vetrivelan - first_name: Clifford B. full_name: Saper, Clifford B. last_name: Saper - first_name: Thomas E. full_name: Scammell, Thomas E. last_name: Scammell - first_name: Plamen Ch. full_name: Ivanov, Plamen Ch. last_name: Ivanov citation: ama: Lombardi F, Gómez-Extremera M, Bernaola-Galván P, et al. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 2020;40(1):171-190. doi:10.1523/jneurosci.1278-19.2019 apa: Lombardi, F., Gómez-Extremera, M., Bernaola-Galván, P., Vetrivelan, R., Saper, C. B., Scammell, T. E., & Ivanov, P. C. (2020). Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1278-19.2019 chicago: Lombardi, Fabrizio, Manuel Gómez-Extremera, Pedro Bernaola-Galván, Ramalingam Vetrivelan, Clifford B. Saper, Thomas E. Scammell, and Plamen Ch. Ivanov. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/jneurosci.1278-19.2019. ieee: F. Lombardi et al., “Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake,” Journal of Neuroscience, vol. 40, no. 1. Society for Neuroscience, pp. 171–190, 2020. ista: Lombardi F, Gómez-Extremera M, Bernaola-Galván P, Vetrivelan R, Saper CB, Scammell TE, Ivanov PC. 2020. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 40(1), 171–190. mla: Lombardi, Fabrizio, et al. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 171–90, doi:10.1523/jneurosci.1278-19.2019. short: F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B. Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190. date_created: 2020-07-05T15:24:51Z date_published: 2020-01-02T00:00:00Z date_updated: 2023-09-05T14:02:55Z day: '02' ddc: - '570' department: - _id: GaTk doi: 10.1523/jneurosci.1278-19.2019 ec_funded: 1 external_id: isi: - '000505167600016' pmid: - '31694962' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-07-22T11:44:48Z date_updated: 2020-07-22T11:44:48Z file_id: '8150' file_name: 2020_JournNeuroscience_Lombardi.pdf file_size: 6646046 relation: main_file success: 1 file_date_updated: 2020-07-22T11:44:48Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 171-190 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Neuroscience publication_identifier: eissn: - 1529-2401 issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2020' ... --- _id: '7650' abstract: - lang: eng text: We consider a dilute, homogeneous Bose gas at positive temperature. The system is investigated in the Gross–Pitaevskii limit, where the scattering length a is so small that the interaction energy is of the same order of magnitude as the spectral gap of the Laplacian, and for temperatures that are comparable to the critical temperature of the ideal gas. We show that the difference between the specific free energy of the interacting system and the one of the ideal gas is to leading order given by 4πa(2ϱ2−ϱ20). Here ϱ denotes the density of the system and ϱ0 is the expected condensate density of the ideal gas. Additionally, we show that the one-particle density matrix of any approximate minimizer of the Gibbs free energy functional is to leading order given by the one of the ideal gas. This in particular proves Bose–Einstein condensation with critical temperature given by the one of the ideal gas to leading order. One key ingredient of our proof is a novel use of the Gibbs variational principle that goes hand in hand with the c-number substitution. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). It is a pleasure to thank Jakob Yngvason for helpful discussions. Financial support by the European Research Council (ERC) under the European Union’sHorizon 2020 research and innovation programme (Grant Agreement No. 694227) is gratefully acknowledged. A. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 836146. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Deuchert A, Seiringer R. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 2020;236(6):1217-1271. doi:10.1007/s00205-020-01489-4 apa: Deuchert, A., & Seiringer, R. (2020). Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01489-4 chicago: Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01489-4. ieee: A. Deuchert and R. Seiringer, “Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature,” Archive for Rational Mechanics and Analysis, vol. 236, no. 6. Springer Nature, pp. 1217–1271, 2020. ista: Deuchert A, Seiringer R. 2020. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 236(6), 1217–1271. mla: Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis, vol. 236, no. 6, Springer Nature, 2020, pp. 1217–71, doi:10.1007/s00205-020-01489-4. short: A. Deuchert, R. Seiringer, Archive for Rational Mechanics and Analysis 236 (2020) 1217–1271. date_created: 2020-04-08T15:18:03Z date_published: 2020-03-09T00:00:00Z date_updated: 2023-09-05T14:18:49Z day: '09' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00205-020-01489-4 ec_funded: 1 external_id: arxiv: - '1901.11363' isi: - '000519415000001' file: - access_level: open_access checksum: b645fb64bfe95bbc05b3eea374109a9c content_type: application/pdf creator: dernst date_created: 2020-11-20T13:17:42Z date_updated: 2020-11-20T13:17:42Z file_id: '8785' file_name: 2020_ArchRatMechanicsAnalysis_Deuchert.pdf file_size: 704633 relation: main_file success: 1 file_date_updated: 2020-11-20T13:17:42Z has_accepted_license: '1' intvolume: ' 236' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1217-1271 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund 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: Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 236 year: '2020' ... --- _id: '8130' abstract: - lang: eng text: We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). I thank Stefan Teufel for helpful remarks and for his involvement in the closely related joint project [10]. Helpful discussions with Serena Cenatiempo and Nikolai Leopold are gratefully acknowledged. This work was supported by the German Research Foundation within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems” and has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. 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 citation: ama: Bossmann L. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 2020;238(11):541-606. doi:10.1007/s00205-020-01548-w apa: Bossmann, L. (2020). Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01548-w chicago: Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01548-w. ieee: L. Bossmann, “Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons,” Archive for Rational Mechanics and Analysis, vol. 238, no. 11. Springer Nature, pp. 541–606, 2020. ista: Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606. mla: Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis, vol. 238, no. 11, Springer Nature, 2020, pp. 541–606, doi:10.1007/s00205-020-01548-w. short: L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606. date_created: 2020-07-18T15:06:35Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-09-05T14:19:06Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00205-020-01548-w ec_funded: 1 external_id: arxiv: - '1907.04547' isi: - '000550164400001' file: - access_level: open_access checksum: cc67a79a67bef441625fcb1cd031db3d content_type: application/pdf creator: dernst date_created: 2020-12-02T08:50:38Z date_updated: 2020-12-02T08:50:38Z file_id: '8826' file_name: 2020_ArchiveRatMech_Bossmann.pdf file_size: 942343 relation: main_file success: 1 file_date_updated: 2020-12-02T08:50:38Z has_accepted_license: '1' intvolume: ' 238' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 541-606 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund 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: Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 238 year: '2020' ... --- _id: '7235' abstract: - lang: eng text: We consider the Fröhlich model of a polaron, and show that its effective mass diverges in thestrong coupling limit. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227; R.S.) is gratefully acknowledged. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Elliott H. full_name: Lieb, Elliott H. last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Lieb EH, Seiringer R. Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. 2020;180:23-33. doi:10.1007/s10955-019-02322-3 apa: Lieb, E. H., & Seiringer, R. (2020). Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-019-02322-3 chicago: Lieb, Elliott H., and Robert Seiringer. “Divergence of the Effective Mass of a Polaron in the Strong Coupling Limit.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-019-02322-3. ieee: E. H. Lieb and R. Seiringer, “Divergence of the effective mass of a polaron in the strong coupling limit,” Journal of Statistical Physics, vol. 180. Springer Nature, pp. 23–33, 2020. ista: Lieb EH, Seiringer R. 2020. Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. 180, 23–33. mla: Lieb, Elliott H., and Robert Seiringer. “Divergence of the Effective Mass of a Polaron in the Strong Coupling Limit.” Journal of Statistical Physics, vol. 180, Springer Nature, 2020, pp. 23–33, doi:10.1007/s10955-019-02322-3. short: E.H. Lieb, R. Seiringer, Journal of Statistical Physics 180 (2020) 23–33. date_created: 2020-01-07T09:42:03Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-05T14:57:29Z day: '01' ddc: - '510' - '530' department: - _id: RoSe doi: 10.1007/s10955-019-02322-3 ec_funded: 1 external_id: isi: - '000556199700003' file: - access_level: open_access checksum: 1e67bee6728592f7bdcea2ad2d9366dc content_type: application/pdf creator: dernst date_created: 2020-11-19T11:13:55Z date_updated: 2020-11-19T11:13:55Z file_id: '8774' file_name: 2020_JourStatPhysics_Lieb.pdf file_size: 279749 relation: main_file success: 1 file_date_updated: 2020-11-19T11:13:55Z has_accepted_license: '1' intvolume: ' 180' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 23-33 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems 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: Divergence of the effective mass of a polaron in the strong coupling limit 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 180 year: '2020' ... --- _id: '7966' abstract: - lang: eng text: "For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).\r\n\r\nFor Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.\r\n\r\nAs our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem." alternative_title: - LNCS article_processing_charge: No author: - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Federico full_name: Giacon, Federico last_name: Giacon - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz citation: ama: 'Auerbach B, Giacon F, Kiltz E. Everybody’s a target: Scalability in public-key encryption. In: Advances in Cryptology – EUROCRYPT 2020. Vol 12107. Springer Nature; 2020:475-506. doi:10.1007/978-3-030-45727-3_16' apa: 'Auerbach, B., Giacon, F., & Kiltz, E. (2020). Everybody’s a target: Scalability in public-key encryption. In Advances in Cryptology – EUROCRYPT 2020 (Vol. 12107, pp. 475–506). Springer Nature. https://doi.org/10.1007/978-3-030-45727-3_16' chicago: 'Auerbach, Benedikt, Federico Giacon, and Eike Kiltz. “Everybody’s a Target: Scalability in Public-Key Encryption.” In Advances in Cryptology – EUROCRYPT 2020, 12107:475–506. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45727-3_16.' ieee: 'B. Auerbach, F. Giacon, and E. Kiltz, “Everybody’s a target: Scalability in public-key encryption,” in Advances in Cryptology – EUROCRYPT 2020, 2020, vol. 12107, pp. 475–506.' ista: 'Auerbach B, Giacon F, Kiltz E. 2020. Everybody’s a target: Scalability in public-key encryption. Advances in Cryptology – EUROCRYPT 2020. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 12107, 475–506.' mla: 'Auerbach, Benedikt, et al. “Everybody’s a Target: Scalability in Public-Key Encryption.” Advances in Cryptology – EUROCRYPT 2020, vol. 12107, Springer Nature, 2020, pp. 475–506, doi:10.1007/978-3-030-45727-3_16.' short: B. Auerbach, F. Giacon, E. Kiltz, in:, Advances in Cryptology – EUROCRYPT 2020, Springer Nature, 2020, pp. 475–506. conference: end_date: 2020-05-15 name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2020-05-11 date_created: 2020-06-15T07:13:37Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-09-05T15:06:40Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-030-45727-3_16 ec_funded: 1 external_id: isi: - '000828688000016' intvolume: ' 12107' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/364 month: '05' oa: 1 oa_version: Submitted Version page: 475-506 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Advances in Cryptology – EUROCRYPT 2020 publication_identifier: eissn: - 1611-3349 isbn: - '9783030457266' - '9783030457273' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Everybody’s a target: Scalability in public-key encryption' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12107 year: '2020' ... --- _id: '8623' abstract: - lang: eng text: We introduce the monitoring of trace properties under assumptions. An assumption limits the space of possible traces that the monitor may encounter. An assumption may result from knowledge about the system that is being monitored, about the environment, or about another, connected monitor. We define monitorability under assumptions and study its theoretical properties. In particular, we show that for every assumption A, the boolean combinations of properties that are safe or co-safe relative to A are monitorable under A. We give several examples and constructions on how an assumption can make a non-monitorable property monitorable, and how an assumption can make a monitorable property monitorable with fewer resources, such as integer registers. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: 'Henzinger TA, Sarac NE. Monitorability under assumptions. In: Runtime Verification. Vol 12399. Springer Nature; 2020:3-18. doi:10.1007/978-3-030-60508-7_1' apa: 'Henzinger, T. A., & Sarac, N. E. (2020). Monitorability under assumptions. In Runtime Verification (Vol. 12399, pp. 3–18). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-60508-7_1' chicago: Henzinger, Thomas A, and Naci E Sarac. “Monitorability under Assumptions.” In Runtime Verification, 12399:3–18. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60508-7_1. ieee: T. A. Henzinger and N. E. Sarac, “Monitorability under assumptions,” in Runtime Verification, Los Angeles, CA, United States, 2020, vol. 12399, pp. 3–18. ista: 'Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.' mla: Henzinger, Thomas A., and Naci E. Sarac. “Monitorability under Assumptions.” Runtime Verification, vol. 12399, Springer Nature, 2020, pp. 3–18, doi:10.1007/978-3-030-60508-7_1. short: T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020, pp. 3–18. conference: end_date: 2020-10-09 location: Los Angeles, CA, United States name: 'RV: Runtime Verification' start_date: 2020-10-06 date_created: 2020-10-07T15:05:37Z date_published: 2020-10-02T00:00:00Z date_updated: 2023-09-05T15:08:26Z day: '02' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-60508-7_1 external_id: isi: - '000728160600001' file: - access_level: open_access checksum: 00661f9b7034f52e18bf24fa552b8194 content_type: application/pdf creator: esarac date_created: 2020-10-15T14:28:06Z date_updated: 2020-10-15T14:28:06Z file_id: '8665' file_name: monitorability.pdf file_size: 478148 relation: main_file success: 1 file_date_updated: 2020-10-15T14:28:06Z has_accepted_license: '1' intvolume: ' 12399' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 3-18 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Runtime Verification publication_identifier: eissn: - 1611-3349 isbn: - '9783030605070' - '9783030605087' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Monitorability under assumptions type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12399 year: '2020' ... --- _id: '8732' abstract: - lang: eng text: 'A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP -complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ , it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Alan M full_name: Arroyo Guevara, Alan M id: 3207FDC6-F248-11E8-B48F-1D18A9856A87 last_name: Arroyo Guevara orcid: 0000-0003-2401-8670 - first_name: Fabian full_name: Klute, Fabian last_name: Klute - first_name: Irene full_name: Parada, Irene last_name: Parada - first_name: Raimund full_name: Seidel, Raimund last_name: Seidel - first_name: Birgit full_name: Vogtenhuber, Birgit last_name: Vogtenhuber - first_name: Tilo full_name: Wiedera, Tilo last_name: Wiedera citation: ama: 'Arroyo Guevara AM, Klute F, Parada I, Seidel R, Vogtenhuber B, Wiedera T. Inserting one edge into a simple drawing is hard. In: Graph-Theoretic Concepts in Computer Science. Vol 12301. Springer Nature; 2020:325-338. doi:10.1007/978-3-030-60440-0_26' apa: 'Arroyo Guevara, A. M., Klute, F., Parada, I., Seidel, R., Vogtenhuber, B., & Wiedera, T. (2020). Inserting one edge into a simple drawing is hard. In Graph-Theoretic Concepts in Computer Science (Vol. 12301, pp. 325–338). Leeds, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-60440-0_26' chicago: Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Raimund Seidel, Birgit Vogtenhuber, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” In Graph-Theoretic Concepts in Computer Science, 12301:325–38. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60440-0_26. ieee: A. M. Arroyo Guevara, F. Klute, I. Parada, R. Seidel, B. Vogtenhuber, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” in Graph-Theoretic Concepts in Computer Science, Leeds, United Kingdom, 2020, vol. 12301, pp. 325–338. ista: 'Arroyo Guevara AM, Klute F, Parada I, Seidel R, Vogtenhuber B, Wiedera T. 2020. Inserting one edge into a simple drawing is hard. Graph-Theoretic Concepts in Computer Science. WG: Workshop on Graph-Theoretic Concepts in Computer Science, LNCS, vol. 12301, 325–338.' mla: Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Graph-Theoretic Concepts in Computer Science, vol. 12301, Springer Nature, 2020, pp. 325–38, doi:10.1007/978-3-030-60440-0_26. short: A.M. Arroyo Guevara, F. Klute, I. Parada, R. Seidel, B. Vogtenhuber, T. Wiedera, in:, Graph-Theoretic Concepts in Computer Science, Springer Nature, 2020, pp. 325–338. conference: end_date: 2020-06-26 location: Leeds, United Kingdom name: 'WG: Workshop on Graph-Theoretic Concepts in Computer Science' start_date: 2020-06-24 date_created: 2020-11-06T08:45:03Z date_published: 2020-10-09T00:00:00Z date_updated: 2023-09-05T15:09:16Z day: '09' department: - _id: UlWa doi: 10.1007/978-3-030-60440-0_26 ec_funded: 1 intvolume: ' 12301' language: - iso: eng month: '10' oa_version: None page: 325-338 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Graph-Theoretic Concepts in Computer Science publication_identifier: eissn: - 1611-3349 isbn: - '9783030604394' - '9783030604400' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Inserting one edge into a simple drawing is hard type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12301 year: '2020' ... --- _id: '10865' abstract: - lang: eng text: "We introduce the notion of Witness Maps as a cryptographic notion of a proof system. A Unique Witness Map (UWM) deterministically maps all witnesses for an \ NP statement to a single representative witness, resulting in a computationally sound, deterministic-prover, non-interactive witness independent proof system. A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable” mode to a CWM.\r\nOur main construction is a DMWM for all NP relations, assuming sub-exponentially secure indistinguishability obfuscation ( iO ), along with standard cryptographic assumptions. The DMWM construction relies on a CWM and a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF), both of which are in turn instantiated based on iO and other primitives. Our instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct, from standard assumptions, Puncturable Digital Signatures and a new primitive called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially secure iO and sub-exponentially secure OWF.\r\nAs an application of our constructions, we show how to use a DMWM to construct the first leakage and tamper-resilient signatures with a deterministic signer, thereby solving a decade old open problem posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs (Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction achieves the optimal leakage rate of 1−o(1) ." acknowledgement: We would like to thank the anonymous reviewers of PKC 2019 for their useful comments and suggestions. We thank Omer Paneth for pointing out to us the connection between Unique Witness Maps (UWM) and Witness encryption (WE). The first author would like to acknowledge Pandu Rangan for his involvement during the initial discussion phase of the project. article_processing_charge: No author: - first_name: Suvradip full_name: Chakraborty, Suvradip id: B9CD0494-D033-11E9-B219-A439E6697425 last_name: Chakraborty - first_name: Manoj full_name: Prabhakaran, Manoj last_name: Prabhakaran - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Chakraborty S, Prabhakaran M, Wichs D. Witness maps and applications. In: Kiayias A, ed. Public-Key Cryptography. Vol 12110. LNCS. Cham: Springer Nature; 2020:220-246. doi:10.1007/978-3-030-45374-9_8' apa: 'Chakraborty, S., Prabhakaran, M., & Wichs, D. (2020). Witness maps and applications. In A. Kiayias (Ed.), Public-Key Cryptography (Vol. 12110, pp. 220–246). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_8' chicago: 'Chakraborty, Suvradip, Manoj Prabhakaran, and Daniel Wichs. “Witness Maps and Applications.” In Public-Key Cryptography, edited by A Kiayias, 12110:220–46. LNCS. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_8.' ieee: 'S. Chakraborty, M. Prabhakaran, and D. Wichs, “Witness maps and applications,” in Public-Key Cryptography, vol. 12110, A. Kiayias, Ed. Cham: Springer Nature, 2020, pp. 220–246.' ista: 'Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications. In: Public-Key Cryptography. vol. 12110, 220–246.' mla: Chakraborty, Suvradip, et al. “Witness Maps and Applications.” Public-Key Cryptography, edited by A Kiayias, vol. 12110, Springer Nature, 2020, pp. 220–46, doi:10.1007/978-3-030-45374-9_8. short: S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key Cryptography, Springer Nature, Cham, 2020, pp. 220–246. date_created: 2022-03-18T11:35:51Z date_published: 2020-04-29T00:00:00Z date_updated: 2023-09-05T15:10:02Z day: '29' doi: 10.1007/978-3-030-45374-9_8 editor: - first_name: A full_name: Kiayias, A last_name: Kiayias intvolume: ' 12110' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2020/090 month: '04' oa: 1 oa_version: Preprint page: 220-246 place: Cham publication: Public-Key Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783030453732' - '9783030453749' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Witness maps and applications type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12110 year: '2020' ... --- _id: '7611' abstract: - lang: eng text: We consider a system of N bosons in the limit N→∞, interacting through singular potentials. For initial data exhibiting Bose–Einstein condensation, the many-body time evolution is well approximated through a quadratic fluctuation dynamics around a cubic nonlinear Schrödinger equation of the condensate wave function. We show that these fluctuations satisfy a (multi-variate) central limit theorem. acknowledgement: "Simone Rademacher acknowledges partial support from the NCCR SwissMAP. This project has received\r\nfunding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nS.R. would like to thank Benjamin Schlein for many fruitful discussions." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Simone Anna Elvira full_name: Rademacher, Simone Anna Elvira id: 856966FE-A408-11E9-977E-802DE6697425 last_name: Rademacher orcid: 0000-0001-5059-4466 citation: ama: Rademacher SAE. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 2020;110:2143-2174. doi:10.1007/s11005-020-01286-w apa: Rademacher, S. A. E. (2020). Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-020-01286-w chicago: Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s11005-020-01286-w. ieee: S. A. E. Rademacher, “Central limit theorem for Bose gases interacting through singular potentials,” Letters in Mathematical Physics, vol. 110. Springer Nature, pp. 2143–2174, 2020. ista: Rademacher SAE. 2020. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 110, 2143–2174. mla: Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics, vol. 110, Springer Nature, 2020, pp. 2143–74, doi:10.1007/s11005-020-01286-w. short: S.A.E. Rademacher, Letters in Mathematical Physics 110 (2020) 2143–2174. date_created: 2020-03-23T11:11:47Z date_published: 2020-03-12T00:00:00Z date_updated: 2023-09-05T15:14:50Z day: '12' ddc: - '510' department: - _id: RoSe doi: 10.1007/s11005-020-01286-w ec_funded: 1 external_id: isi: - '000551556000006' file: - access_level: open_access checksum: 3bdd41f10ad947b67a45b98f507a7d4a content_type: application/pdf creator: dernst date_created: 2020-11-20T12:04:26Z date_updated: 2020-11-20T12:04:26Z file_id: '8784' file_name: 2020_LettersMathPhysics_Rademacher.pdf file_size: 478683 relation: main_file success: 1 file_date_updated: 2020-11-20T12:04:26Z has_accepted_license: '1' intvolume: ' 110' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 2143-2174 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund 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: Central limit theorem for Bose gases interacting through singular potentials 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 110 year: '2020' ... --- _id: '7236' abstract: - lang: eng text: The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study. article_number: e01397 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: Lucy full_name: Schroeder, Lucy last_name: Schroeder - first_name: Marjorie G. full_name: Weber, Marjorie G. last_name: Weber - first_name: Douglas W. full_name: Schemske, Douglas W. last_name: Schemske citation: ama: Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 2020;90(1). doi:10.1002/ecm.1397 apa: Baskett, C., Schroeder, L., Weber, M. G., & Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. Wiley. https://doi.org/10.1002/ecm.1397 chicago: Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs. Wiley, 2020. https://doi.org/10.1002/ecm.1397. ieee: C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” Ecological Monographs, vol. 90, no. 1. Wiley, 2020. ista: Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397. mla: Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs, vol. 90, no. 1, e01397, Wiley, 2020, doi:10.1002/ecm.1397. short: C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020). date_created: 2020-01-07T12:47:07Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-09-05T15:43:19Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1002/ecm.1397 ec_funded: 1 external_id: isi: - '000508511600001' file: - access_level: open_access checksum: ab8130c6e68101f5a091d05324c36f08 content_type: application/pdf creator: dernst date_created: 2020-02-10T08:18:14Z date_updated: 2020-07-14T12:47:54Z file_id: '7469' file_name: 2020_EcologMono_Baskett.pdf file_size: 537941 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 90' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '02' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Ecological Monographs publication_identifier: eissn: - 1557-7015 issn: - 0012-9615 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 90 year: '2020' ... --- _id: '7697' abstract: - lang: eng text: "* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.\r\n* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.\r\n* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.\r\n* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Corinna full_name: Hartinger, Corinna id: AEFB2266-8ABF-11EA-AA39-812C3623CBE4 last_name: Hartinger orcid: 0000-0003-1618-2737 - first_name: Xiaojuan full_name: Wang, Xiaojuan last_name: Wang - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 2020;227(5):1406-1416. doi:10.1111/nph.16629 apa: Zhang, Y., Hartinger, C., Wang, X., & Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. Wiley. https://doi.org/10.1111/nph.16629 chicago: Zhang, Yuzhou, Corinna Hartinger, Xiaojuan Wang, and Jiří Friml. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16629. ieee: Y. Zhang, C. Hartinger, X. Wang, and J. Friml, “Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters,” New Phytologist, vol. 227, no. 5. Wiley, pp. 1406–1416, 2020. ista: Zhang Y, Hartinger C, Wang X, Friml J. 2020. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 227(5), 1406–1416. mla: Zhang, Yuzhou, et al. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist, vol. 227, no. 5, Wiley, 2020, pp. 1406–16, doi:10.1111/nph.16629. short: Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416. date_created: 2020-04-30T08:43:29Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-05T15:46:04Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.16629 ec_funded: 1 external_id: isi: - '000534092400001' pmid: - '32350870' file: - access_level: open_access checksum: 8e8150dbbba8cb65b72f81d1f0864b8b content_type: application/pdf creator: dernst date_created: 2020-11-24T12:19:38Z date_updated: 2020-11-24T12:19:38Z file_id: '8799' file_name: 2020_09_NewPhytologist_Zhang.pdf file_size: 3643395 relation: main_file success: 1 file_date_updated: 2020-11-24T12:19:38Z has_accepted_license: '1' intvolume: ' 227' isi: 1 issue: '5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1406-1416 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 227 year: '2020' ... --- _id: '8765' abstract: - lang: eng text: This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate. acknowledged_ssus: - _id: ScienComp acknowledgement: "We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176." article_processing_charge: No article_type: original author: - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 2020;39(2):89-99. doi:10.1111/cgf.13914 apa: Schreck, C., & Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13914 chicago: Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.13914. ieee: C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” Computer Graphics Forum, vol. 39, no. 2. Wiley, pp. 89–99, 2020. ista: Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99. mla: Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:10.1111/cgf.13914. short: C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99. date_created: 2020-11-17T09:35:10Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-09-05T16:00:13Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.13914 ec_funded: 1 external_id: isi: - '000548709600008' file: - access_level: open_access checksum: 7605f605acd84d0942b48bc7a1c2d72e content_type: application/pdf creator: dernst date_created: 2020-11-23T09:05:13Z date_updated: 2020-11-23T09:05:13Z file_id: '8796' file_name: 2020_poff_revisited.pdf file_size: 38969122 relation: main_file success: 1 file_date_updated: 2020-11-23T09:05:13Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '2' keyword: - Computer Networks and Communications language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 89-99 project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: Computer Graphics Forum publication_identifier: eissn: - 1467-8659 issn: - 0167-7055 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: A practical method for animating anisotropic elastoplastic materials type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 39 year: '2020' ... --- _id: '8057' abstract: - lang: eng text: Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability. article_processing_charge: No article_type: original author: - first_name: Roza full_name: Bouchal, Roza last_name: Bouchal - first_name: Zhujie full_name: Li, Zhujie last_name: Li - first_name: Chandra full_name: Bongu, Chandra last_name: Bongu - first_name: Steven full_name: Le Vot, Steven last_name: Le Vot - first_name: Romain full_name: Berthelot, Romain last_name: Berthelot - first_name: Benjamin full_name: Rotenberg, Benjamin last_name: Rotenberg - first_name: Frederic full_name: Favier, Frederic last_name: Favier - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Mathieu full_name: Salanne, Mathieu last_name: Salanne - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine citation: ama: Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 2020;132(37):16047-16051. doi:10.1002/ange.202005378 apa: Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202005378 chicago: Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Frederic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie. Wiley, 2020. https://doi.org/10.1002/ange.202005378. ieee: R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie, vol. 132, no. 37. Wiley, pp. 16047–16051, 2020. ista: Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 132(37), 16047–16051. mla: Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie, vol. 132, no. 37, Wiley, 2020, pp. 16047–51, doi:10.1002/ange.202005378. short: R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie 132 (2020) 16047–16051. date_created: 2020-06-29T16:15:49Z date_published: 2020-09-07T00:00:00Z date_updated: 2023-09-05T15:47:50Z day: '07' ddc: - '540' - '541' department: - _id: StFr doi: 10.1002/ange.202005378 file: - access_level: open_access checksum: 7dd0a56f6bd5de08ea75b1ec388c91bc content_type: application/pdf creator: dernst date_created: 2020-09-17T08:59:43Z date_updated: 2020-09-17T08:59:43Z file_id: '8401' file_name: 2020_AngChemieDE_Bouchal.pdf file_size: 1904552 relation: main_file success: 1 file_date_updated: 2020-09-17T08:59:43Z has_accepted_license: '1' intvolume: ' 132' issue: '37' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 16047-16051 publication: Angewandte Chemie publication_identifier: eissn: - 1521-3757 issn: - 0044-8249 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 132 year: '2020' ... --- _id: '7343' abstract: - lang: eng text: Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level. acknowledged_ssus: - _id: LifeSc acknowledgement: "We thank Bernhardt Steinwender and Jorgen Eilenberg for the fungal strains, Xavier Espadaler, Mireia Diaz, Christiane Wanke, Lumi Viljakainen and the Social Immunity Team at IST Austria, for help with ant collection, and Wanda Gorecka and Gertraud Stift of the IST Austria Life Science Facility for technical support. We are thankful to Dieter Ebert for input at all stages of the project, Roger Mundry for statistical advice, Hinrich Schulenburg, Paul Schmid-Hempel, Yuko\r\nUlrich and Joachim Kurtz for project discussion, Bor Kavcic for advice on growth curves, Marcus Roper for advice on modelling work and comments on the manuscript, as well as Marjon de Vos, Weini Huang and the Social Immunity Team for comments on the manuscript.\r\nThis study was funded by the German Research Foundation (DFG) within the Priority Programme 1399 Host-parasite Coevolution (CR 118/3 to S.C.) and the People Programme\r\n(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no 291734 (ISTFELLOW to B.M.). " article_processing_charge: Yes (via OA deal) article_type: letter_note author: - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Elisabeth full_name: Naderlinger, Elisabeth id: 31757262-F248-11E8-B48F-1D18A9856A87 last_name: Naderlinger - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 2020;23(3):565-574. doi:10.1111/ele.13458 apa: Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13458 chicago: Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13458. ieee: B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 565–574, 2020. ista: Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 23(3), 565–574. mla: Milutinovic, Barbara, et al. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 565–74, doi:10.1111/ele.13458. short: B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, Ecology Letters 23 (2020) 565–574. date_created: 2020-01-20T13:32:12Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-05T16:04:49Z day: '01' ddc: - '570' department: - _id: SyCr - _id: KrCh doi: 10.1111/ele.13458 ec_funded: 1 external_id: isi: - '000507515900001' file: - access_level: open_access checksum: 0cd8be386fa219db02845b7c3991ce04 content_type: application/pdf creator: dernst date_created: 2020-11-19T11:27:10Z date_updated: 2020-11-19T11:27:10Z file_id: '8776' file_name: 2020_EcologyLetters_Milutinovic.pdf file_size: 561749 relation: main_file success: 1 file_date_updated: 2020-11-19T11:27:10Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 565-574 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution publication: Ecology Letters publication_identifier: eissn: - 1461-0248 issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/social-ants-shapes-disease-outcome/ record: - id: '13060' relation: research_data status: public scopus_import: '1' status: public title: Social immunity modulates competition between coinfecting pathogens tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2020' ... --- _id: '8099' abstract: - lang: eng text: Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: William J full_name: Gammerdinger, William J id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87 last_name: Gammerdinger orcid: 0000-0001-9638-1220 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: 'Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from  sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525. doi:10.1111/1755-0998.13210' apa: 'Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in FST estimators: A case study from  sex chromosomes. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13210' chicago: 'Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” Molecular Ecology Resources. Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.' ieee: 'W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from  sex chromosomes,” Molecular Ecology Resources, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.' ista: 'Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from  sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.' mla: 'Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:10.1111/1755-0998.13210.' short: W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525. date_created: 2020-07-07T08:56:16Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-09-05T16:07:08Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1111/1755-0998.13210 ec_funded: 1 external_id: isi: - '000545451200001' pmid: - '32543001' file: - access_level: open_access checksum: 3d87ebb8757dcd504f20c618b72e6575 content_type: application/pdf creator: dernst date_created: 2020-11-26T11:46:43Z date_updated: 2020-11-26T11:46:43Z file_id: '8814' file_name: 2020_MolecularEcologyRes_Gammerdinger.pdf file_size: 820428 relation: main_file success: 1 file_date_updated: 2020-11-26T11:46:43Z has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1517-1525 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Molecular Ecology Resources publication_identifier: eissn: - 1755-0998 issn: - 1755-098X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Disagreement in FST estimators: A case study from sex chromosomes' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 20 year: '2020' ... --- _id: '7847' abstract: - lang: eng text: 'Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities nearing 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ''free'' and ''bound'' water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability. ' article_processing_charge: No article_type: original author: - first_name: Roza full_name: Bouchal, Roza last_name: Bouchal - first_name: Zhujie full_name: Li, Zhujie last_name: Li - first_name: Chandra full_name: Bongu, Chandra last_name: Bongu - first_name: Steven full_name: Le Vot, Steven last_name: Le Vot - first_name: Romain full_name: Berthelot, Romain last_name: Berthelot - first_name: Benjamin full_name: Rotenberg, Benjamin last_name: Rotenberg - first_name: Fréderic full_name: Favier, Fréderic last_name: Favier - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Mathieu full_name: Salanne, Mathieu last_name: Salanne - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine citation: ama: Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 2020;59(37):15913-1591. doi:10.1002/anie.202005378 apa: Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202005378 chicago: Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Fréderic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202005378. ieee: R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie International Edition, vol. 59, no. 37. Wiley, pp. 15913–1591, 2020. ista: Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 59(37), 15913–1591. mla: Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition, vol. 59, no. 37, Wiley, 2020, pp. 15913–1591, doi:10.1002/anie.202005378. short: R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie International Edition 59 (2020) 15913–1591. date_created: 2020-05-14T21:00:30Z date_published: 2020-09-07T00:00:00Z date_updated: 2023-09-05T16:02:53Z day: '07' ddc: - '540' - '546' department: - _id: StFr doi: 10.1002/anie.202005378 external_id: isi: - '000541488700001' pmid: - '32390281' file: - access_level: open_access checksum: 7b6c2fc20e9b0ff4353352f7a7004e2d content_type: application/pdf creator: dernst date_created: 2020-09-17T08:57:16Z date_updated: 2020-09-17T08:57:16Z file_id: '8400' file_name: 2020_AngChemieINT_Buchal.pdf file_size: 1966184 relation: main_file success: 1 file_date_updated: 2020-09-17T08:57:16Z has_accepted_license: '1' intvolume: ' 59' isi: 1 issue: '37' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 15913-1591 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 59 year: '2020' ... --- _id: '7224' abstract: - lang: eng text: 'Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Nerea full_name: Abrego, Nerea last_name: Abrego - first_name: Otso full_name: Ovaskainen, Otso last_name: Ovaskainen citation: ama: Rybicki J, Abrego N, Ovaskainen O. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 2020;23(3):506-517. doi:10.1111/ele.13450 apa: Rybicki, J., Abrego, N., & Ovaskainen, O. (2020). Habitat fragmentation and species diversity in competitive communities. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13450 chicago: Rybicki, Joel, Nerea Abrego, and Otso Ovaskainen. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13450. ieee: J. Rybicki, N. Abrego, and O. Ovaskainen, “Habitat fragmentation and species diversity in competitive communities,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 506–517, 2020. ista: Rybicki J, Abrego N, Ovaskainen O. 2020. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 23(3), 506–517. mla: Rybicki, Joel, et al. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 506–17, doi:10.1111/ele.13450. short: J. Rybicki, N. Abrego, O. Ovaskainen, Ecology Letters 23 (2020) 506–517. date_created: 2020-01-04T11:04:30Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-05T16:04:30Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.1111/ele.13450 ec_funded: 1 external_id: isi: - '000503625200001' file: - access_level: open_access checksum: 372f67f2744f4b6049e9778364766c22 content_type: application/pdf creator: dernst date_created: 2020-02-14T12:02:50Z date_updated: 2020-07-14T12:47:54Z file_id: '7486' file_name: 2020_EcologyLetters_Rybicki.pdf file_size: 3005474 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 506-517 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 26A5D39A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '840605' name: Coordination in constrained and natural distributed systems publication: Ecology Letters publication_identifier: eissn: - 1461-0248 issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Habitat fragmentation and species diversity in competitive communities 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2020' ... --- _id: '8329' abstract: - lang: eng text: We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles. acknowledgement: The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429). article_processing_charge: No article_type: original author: - first_name: Werner full_name: Schlemmer, Werner last_name: Schlemmer - first_name: Philipp full_name: Nothdurft, Philipp last_name: Nothdurft - first_name: Alina full_name: Petzold, Alina last_name: Petzold - first_name: Philipp full_name: Frühwirt, Philipp last_name: Frühwirt - first_name: Max full_name: Schmallegger, Max last_name: Schmallegger - first_name: Georg full_name: Gescheidt-Demner, Georg last_name: Gescheidt-Demner - first_name: Roland full_name: Fischer, Roland last_name: Fischer - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Wolfgang full_name: Kern, Wolfgang last_name: Kern - first_name: Stefan full_name: Spirk, Stefan last_name: Spirk citation: ama: Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 2020;59(51):22943-22946. doi:10.1002/anie.202008253 apa: Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202008253 chicago: Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger, Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202008253. ieee: W. Schlemmer et al., “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” Angewandte Chemie International Edition, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020. ista: Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 59(51), 22943–22946. mla: Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253. short: W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946. date_created: 2020-09-03T16:10:56Z date_published: 2020-12-14T00:00:00Z date_updated: 2023-09-05T16:03:47Z day: '14' department: - _id: StFr doi: 10.1002/anie.202008253 external_id: isi: - '000576148700001' intvolume: ' 59' isi: 1 issue: '51' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/anie.202008253 month: '12' oa: 1 oa_version: Published Version page: 22943-22946 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9780' relation: research_data status: public scopus_import: '1' status: public title: 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 59 year: '2020' ... --- _id: '13060' abstract: - lang: eng text: Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity ­– influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level. article_processing_charge: No author: - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Elisabeth full_name: Naderlinger, Elisabeth id: 31757262-F248-11E8-B48F-1D18A9856A87 last_name: Naderlinger - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318 apa: Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318 chicago: Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318. ieee: B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020. ista: Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318. mla: Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318. short: B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020). date_created: 2023-05-23T16:11:22Z date_published: 2020-12-19T00:00:00Z date_updated: 2023-09-05T16:04:48Z day: '19' ddc: - '570' department: - _id: SyCr - _id: KrCh doi: 10.5061/DRYAD.CRJDFN318 license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.crjdfn318 month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '7343' relation: used_in_publication status: public status: public title: Social immunity modulates competition between coinfecting pathogens tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9780' abstract: - lang: eng text: "PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°" article_processing_charge: No author: - first_name: Werner full_name: Schlemmer, Werner last_name: Schlemmer - first_name: Philipp full_name: Nothdurft, Philipp last_name: Nothdurft - first_name: Alina full_name: Petzold, Alina last_name: Petzold - first_name: Gisbert full_name: Riess, Gisbert last_name: Riess - first_name: Philipp full_name: Frühwirt, Philipp last_name: Frühwirt - first_name: Max full_name: Schmallegger, Max last_name: Schmallegger - first_name: Georg full_name: Gescheidt-Demner, Georg last_name: Gescheidt-Demner - first_name: Roland full_name: Fischer, Roland last_name: Fischer - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Wolfgang full_name: Kern, Wolfgang last_name: Kern - first_name: Stefan full_name: Spirk, Stefan last_name: Spirk citation: ama: 'Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk' apa: 'Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk' chicago: 'Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.' ieee: 'W. Schlemmer et al., “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.' ista: 'Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, 10.5517/ccdc.csd.cc24vsrk.' mla: 'Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure Determination. CCDC, 2020, doi:10.5517/ccdc.csd.cc24vsrk.' short: W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020). date_created: 2021-08-06T07:41:07Z date_published: 2020-03-22T00:00:00Z date_updated: 2023-09-05T16:03:47Z day: '22' department: - _id: StFr doi: 10.5517/ccdc.csd.cc24vsrk main_file_link: - open_access: '1' url: https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk month: '03' oa: 1 oa_version: Published Version publisher: CCDC related_material: record: - id: '8329' relation: used_in_publication status: public status: public title: 'CCDC 1991959: Experimental Crystal Structure Determination' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '7207' abstract: - lang: eng text: The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD. article_processing_charge: No article_type: original author: - first_name: Alejandro full_name: Martín-Belmonte, Alejandro last_name: Martín-Belmonte - first_name: Carolina full_name: Aguado, Carolina last_name: Aguado - first_name: Rocío full_name: Alfaro-Ruíz, Rocío last_name: Alfaro-Ruíz - first_name: Ana Esther full_name: Moreno-Martínez, Ana Esther last_name: Moreno-Martínez - first_name: Luis full_name: De La Ossa, Luis last_name: De La Ossa - first_name: José full_name: Martínez-Hernández, José last_name: Martínez-Hernández - first_name: Alain full_name: Buisson, Alain last_name: Buisson - first_name: Simon full_name: Früh, Simon last_name: Früh - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Rafael full_name: Luján, Rafael last_name: Luján citation: ama: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 2020;30(3):554-575. doi:10.1111/bpa.12802 apa: Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. Wiley. https://doi.org/10.1111/bpa.12802 chicago: Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology. Wiley, 2020. https://doi.org/10.1111/bpa.12802. ieee: A. Martín-Belmonte et al., “Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease,” Brain Pathology, vol. 30, no. 3. Wiley, pp. 554–575, 2020. ista: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Früh S, Bettler B, Shigemoto R, Fukazawa Y, Luján R. 2020. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 30(3), 554–575. mla: Martín-Belmonte, Alejandro, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology, vol. 30, no. 3, Wiley, 2020, pp. 554–75, doi:10.1111/bpa.12802. short: A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, S. Früh, B. Bettler, R. Shigemoto, Y. Fukazawa, R. Luján, Brain Pathology 30 (2020) 554–575. date_created: 2019-12-22T23:00:43Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-09-06T14:48:01Z day: '01' ddc: - '570' department: - _id: RySh doi: 10.1111/bpa.12802 ec_funded: 1 external_id: isi: - '000502270900001' pmid: - '31729777' file: - access_level: open_access checksum: 549cc1b18f638a21d17a939ba5563fa9 content_type: application/pdf creator: dernst date_created: 2020-09-22T09:47:19Z date_updated: 2020-09-22T09:47:19Z file_id: '8554' file_name: 2020_BrainPathology_MartinBelmonte.pdf file_size: 4220935 relation: main_file success: 1 file_date_updated: 2020-09-22T09:47:19Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 554-575 pmid: 1 project: - _id: 25CBA828-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '720270' name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1) - _id: 26436750-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '785907' name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2) publication: Brain Pathology publication_identifier: eissn: - '17503639' issn: - '10156305' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2020' ... --- _id: '7205' abstract: - lang: eng text: Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females. article_processing_charge: No article_type: original author: - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Zuzanna full_name: Zagrodzka, Zuzanna last_name: Zagrodzka - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570 apa: Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570 chicago: Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570. ieee: K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020. ista: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351. mla: Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570. short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351. date_created: 2019-12-22T23:00:43Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-06T14:48:57Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.13570 external_id: isi: - '000500954800001' pmid: - '31724256' file: - access_level: open_access checksum: 7534ff0839709c0c5265c12d29432f03 content_type: application/pdf creator: dernst date_created: 2020-09-22T09:42:18Z date_updated: 2020-09-22T09:42:18Z file_id: '8553' file_name: 2020_EvolBiology_Johannesson.pdf file_size: 885611 relation: main_file success: 1 file_date_updated: 2020-09-22T09:42:18Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 342-351 pmid: 1 publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13067' relation: research_data status: public scopus_import: '1' status: public title: Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 33 year: '2020' ... --- _id: '7227' abstract: - lang: eng text: Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation. acknowledgement: We thank Alexandra Schauer, Nicoletta Petridou and Feyza Nur Arslan for comments on the manuscript. Research in the Heisenberg laboratory is supported by an ERC Advanced Grant (MECSPEC 742573), ANR/FWF (I03601) and FWF/DFG (I03196) International Cooperation Grants. D. Pinheiro acknowledges a fellowship from EMBO ALTF (850-2017) and is currently supported by HFSP LTF (LT000429/2018-L2). alternative_title: - Current Topics in Developmental Biology article_processing_charge: No author: - first_name: Diana C full_name: Nunes Pinheiro, Diana C id: 2E839F16-F248-11E8-B48F-1D18A9856A87 last_name: Nunes Pinheiro orcid: 0000-0003-4333-7503 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Nunes Pinheiro DC, Heisenberg C-PJ. Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Vol 136. Elsevier; 2020:343-375. doi:10.1016/bs.ctdb.2019.10.009' apa: 'Nunes Pinheiro, D. C., & Heisenberg, C.-P. J. (2020). Zebrafish gastrulation: Putting fate in motion. In Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 343–375). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.10.009' chicago: 'Nunes Pinheiro, Diana C, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” In Gastrulation: From Embryonic Pattern to Form, 136:343–75. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.10.009.' ieee: 'D. C. Nunes Pinheiro and C.-P. J. Heisenberg, “Zebrafish gastrulation: Putting fate in motion,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–375.' ista: 'Nunes Pinheiro DC, Heisenberg C-PJ. 2020.Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Current Topics in Developmental Biology, vol. 136, 343–375.' mla: 'Nunes Pinheiro, Diana C., and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–75, doi:10.1016/bs.ctdb.2019.10.009.' short: 'D.C. Nunes Pinheiro, C.-P.J. Heisenberg, in:, Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 343–375.' date_created: 2020-01-05T23:00:46Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-09-06T14:54:36Z day: '01' department: - _id: CaHe doi: 10.1016/bs.ctdb.2019.10.009 ec_funded: 1 external_id: isi: - '000611830600013' pmid: - '31959295' intvolume: ' 136' isi: 1 language: - iso: eng month: '06' oa_version: None page: 343-375 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 2646861A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03601 name: Control of embryonic cleavage pattern - _id: 2608FC64-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03196 name: Control of epithelial cell layer spreading in zebrafish - _id: 266BC5CE-B435-11E9-9278-68D0E5697425 grant_number: LT000429 name: Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation - _id: 26520D1E-B435-11E9-9278-68D0E5697425 grant_number: ALTF 850-2017 name: Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation publication: 'Gastrulation: From Embryonic Pattern to Form' publication_identifier: issn: - '00702153' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Zebrafish gastrulation: Putting fate in motion' type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 136 year: '2020' ... --- _id: '7417' abstract: - lang: eng text: Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development. article_number: e1687185 article_processing_charge: No article_type: original author: - first_name: Scott A full_name: Sinclair, Scott A id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87 last_name: Sinclair orcid: 0000-0002-4566-0593 - first_name: S. full_name: Gille, S. last_name: Gille - first_name: M. full_name: Pauly, M. last_name: Pauly - first_name: U. full_name: Krämer, U. last_name: Krämer citation: ama: Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687185 apa: Sinclair, S. A., Gille, S., Pauly, M., & Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. Informa UK Limited. https://doi.org/10.1080/15592324.2019.1687185 chicago: Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior. Informa UK Limited, 2020. https://doi.org/10.1080/15592324.2019.1687185. ieee: S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” Plant Signaling & Behavior, vol. 15, no. 1. Informa UK Limited, 2020. ista: Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 15(1), e1687185. mla: Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:10.1080/15592324.2019.1687185. short: S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling & Behavior 15 (2020). date_created: 2020-01-30T10:14:14Z date_published: 2020-01-01T00:00:00Z date_updated: 2023-09-06T15:23:04Z day: '01' department: - _id: JiFr doi: 10.1080/15592324.2019.1687185 external_id: isi: - '000494907500001' pmid: - '31696770' intvolume: ' 15' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154 month: '01' oa: 1 oa_version: Submitted Version pmid: 1 publication: Plant Signaling & Behavior publication_identifier: issn: - 1559-2324 publication_status: published publisher: Informa UK Limited quality_controlled: '1' scopus_import: '1' status: public title: Regulation of acetylation of plant cell wall components is complex and responds to external stimuli type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 15 year: '2020' ... --- _id: '6185' abstract: - lang: eng text: For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969). acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work. article_processing_charge: Yes (via OA deal) 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: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: 'Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 2020;378:1203-1278. doi:10.1007/s00220-019-03657-4' apa: 'Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03657-4' chicago: 'Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03657-4.' ieee: 'L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” Communications in Mathematical Physics, vol. 378. Springer Nature, pp. 1203–1278, 2020.' ista: 'Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278.' mla: 'Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:10.1007/s00220-019-03657-4.' short: L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278. date_created: 2019-03-28T10:21:15Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-07T12:54:12Z day: '01' ddc: - '530' - '510' department: - _id: LaEr doi: 10.1007/s00220-019-03657-4 ec_funded: 1 external_id: arxiv: - '1809.03971' isi: - '000529483000001' file: - access_level: open_access checksum: c3a683e2afdcea27afa6880b01e53dc2 content_type: application/pdf creator: dernst date_created: 2020-11-18T11:14:37Z date_updated: 2020-11-18T11:14:37Z file_id: '8771' file_name: 2020_CommMathPhysics_Erdoes.pdf file_size: 2904574 relation: main_file success: 1 file_date_updated: 2020-11-18T11:14:37Z has_accepted_license: '1' intvolume: ' 378' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1203-1278 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '6179' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Cusp universality for random matrices I: Local law and the complex Hermitian case' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 378 year: '2020' ... --- _id: '7629' abstract: - lang: eng text: "This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dominik L full_name: Forkert, Dominik L id: 35C79D68-F248-11E8-B48F-1D18A9856A87 last_name: Forkert citation: ama: Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629 apa: Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629 chicago: Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629. ieee: D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020. ista: Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. mla: Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629. short: D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020. date_created: 2020-04-02T06:40:23Z date_published: 2020-03-31T00:00:00Z date_updated: 2023-09-07T13:03:12Z day: '31' ddc: - '510' degree_awarded: PhD department: - _id: JaMa doi: 10.15479/AT:ISTA:7629 ec_funded: 1 file: - access_level: open_access checksum: c814a1a6195269ca6fe48b0dca45ae8a content_type: application/pdf creator: dernst date_created: 2020-04-14T10:47:59Z date_updated: 2020-07-14T12:48:01Z file_id: '7657' file_name: Thesis_Forkert_PDFA.pdf file_size: 3297129 relation: main_file - access_level: closed checksum: ceafb53f923d1b5bdf14b2b0f22e4a81 content_type: application/x-zip-compressed creator: dernst date_created: 2020-04-14T10:47:59Z date_updated: 2020-07-14T12:48:01Z file_id: '7658' file_name: Thesis_Forkert_source.zip file_size: 1063908 relation: source_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '154' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8574' abstract: - lang: eng text: "This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep citation: ama: Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574 apa: Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574 chicago: Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574. ieee: E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020. ista: Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria. mla: Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574. short: E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020. date_created: 2020-09-28T07:33:38Z date_published: 2020-09-20T00:00:00Z date_updated: 2023-09-07T13:11:39Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: NiBa doi: 10.15479/AT:ISTA:8574 file: - access_level: open_access checksum: 20e71f015fbbd78fea708893ad634ed0 content_type: application/pdf creator: dernst date_created: 2020-09-28T07:25:35Z date_updated: 2020-09-28T07:25:35Z file_id: '8575' file_name: thesis_EnikoSzep_final.pdf file_size: 6354833 relation: main_file success: 1 - access_level: closed checksum: a8de2c14a1bb4e53c857787efbb289e1 content_type: application/x-zip-compressed creator: dernst date_created: 2020-09-28T07:25:37Z date_updated: 2020-09-28T07:25:37Z file_id: '8576' file_name: thesisFiles_EnikoSzep.zip file_size: 23020401 relation: source_file file_date_updated: 2020-09-28T07:25:37Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '158' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Local adaptation in metapopulations type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7514' abstract: - lang: eng text: "We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Simon full_name: Mayer, Simon id: 30C4630A-F248-11E8-B48F-1D18A9856A87 last_name: Mayer citation: ama: Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514 apa: Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514 chicago: Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514. ieee: S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020. ista: Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. mla: Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514. short: S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020. date_created: 2020-02-24T09:17:27Z date_published: 2020-02-24T00:00:00Z date_updated: 2023-09-07T13:12:42Z day: '24' ddc: - '510' degree_awarded: PhD department: - _id: RoSe - _id: GradSch doi: 10.15479/AT:ISTA:7514 ec_funded: 1 file: - access_level: open_access checksum: b4de7579ddc1dbdd44ff3f17c48395f6 content_type: application/pdf creator: dernst date_created: 2020-02-24T09:15:06Z date_updated: 2020-07-14T12:47:59Z file_id: '7515' file_name: thesis.pdf file_size: 1563429 relation: main_file - access_level: closed checksum: ad7425867b52d7d9e72296e87bc9cb67 content_type: application/x-zip-compressed creator: dernst date_created: 2020-02-24T09:15:16Z date_updated: 2020-07-14T12:47:59Z file_id: '7516' file_name: thesis_source.zip file_size: 2028038 relation: source_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '148' project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7524' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: The free energy of a dilute two-dimensional Bose gas 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8353' abstract: - lang: eng text: "Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner." acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: ScienComp acknowledgement: "I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia full_name: Steiner, Julia id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87 last_name: Steiner orcid: 0000-0003-0493-3775 citation: ama: Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353 apa: Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353 chicago: Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353. ieee: J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020. ista: Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. mla: Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353. short: J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020. date_created: 2020-09-09T14:27:01Z date_published: 2020-09-09T00:00:00Z date_updated: 2023-09-07T13:14:09Z day: '09' ddc: - '572' degree_awarded: PhD department: - _id: LeSa doi: 10.15479/AT:ISTA:8353 file: - access_level: open_access checksum: 2388d7e6e7a4d364c096fa89f305c3de content_type: application/pdf creator: jsteiner date_created: 2020-09-09T14:22:35Z date_updated: 2021-09-16T12:40:56Z file_id: '8354' file_name: Thesis_Julia_Steiner_pdfA.pdf file_size: 117547589 relation: main_file - access_level: closed checksum: ba112f957b7145462d0ab79044873ee9 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jsteiner date_created: 2020-09-09T14:23:25Z date_updated: 2020-09-15T08:48:37Z file_id: '8355' file_name: Thesis_Julia_Steiner.docx file_size: 223328668 relation: source_file file_date_updated: 2021-09-16T12:40:56Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: None page: '191' project: - _id: 26169496-B435-11E9-9278-68D0E5697425 grant_number: '24741' name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8284' relation: part_of_dissertation status: public status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8589' abstract: - lang: eng text: The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han citation: ama: Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589 apa: Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589 chicago: Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589. ieee: H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020. ista: Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. mla: Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589. short: H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020. date_created: 2020-09-30T14:50:51Z date_published: 2020-09-30T00:00:00Z date_updated: 2023-09-07T13:13:05Z day: '30' ddc: - '580' degree_awarded: PhD department: - _id: JiFr doi: 10.15479/AT:ISTA:8589 file: - access_level: closed checksum: c4bda1947d4c09c428ac9ce667b02327 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2020-09-30T14:50:20Z date_updated: 2020-09-30T14:50:20Z file_id: '8590' file_name: 2020_Han_Thesis.docx file_size: 49198118 relation: source_file - access_level: open_access checksum: 3f4f5d1718c2230adf30639ecaf8a00b content_type: application/pdf creator: dernst date_created: 2020-09-30T14:49:59Z date_updated: 2021-10-01T13:33:02Z file_id: '8591' file_name: 2020_Han_Thesis.pdf file_size: 15513963 relation: main_file file_date_updated: 2021-10-01T13:33:02Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '164' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7643' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Novel insights into PIN polarity regulation during Arabidopsis development type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8284' abstract: - lang: eng text: Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc acknowledgement: This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. article_number: e59407 article_processing_charge: No article_type: original author: - first_name: Julia full_name: Steiner, Julia id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87 last_name: Steiner orcid: 0000-0003-0493-3775 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407 apa: Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407 chicago: Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407. ieee: J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020. ista: Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407. mla: Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407. short: J. Steiner, L.A. Sazanov, ELife 9 (2020). date_created: 2020-08-24T06:24:04Z date_published: 2020-07-31T00:00:00Z date_updated: 2023-09-07T13:14:08Z day: '31' ddc: - '570' department: - _id: LeSa doi: 10.7554/eLife.59407 external_id: isi: - '000562123600001' pmid: - '32735215' file: - access_level: open_access checksum: b3656d14d5ddbb9d26e3074eea2d0c15 content_type: application/pdf creator: cziletti date_created: 2020-08-24T13:31:53Z date_updated: 2020-08-24T13:31:53Z file_id: '8289' file_name: 2020_eLife_Steiner.pdf file_size: 7320493 relation: main_file success: 1 file_date_updated: 2020-08-24T13:31:53Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26169496-B435-11E9-9278-68D0E5697425 grant_number: '24741' name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/ record: - id: '8353' relation: dissertation_contains status: public scopus_import: '1' status: public title: Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '8155' abstract: - lang: eng text: "In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. " acknowledgement: For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 citation: ama: Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155 apa: Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155 chicago: Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155. ieee: R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020. ista: Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. mla: Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155. short: R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020. date_created: 2020-07-23T09:51:28Z date_published: 2020-07-24T00:00:00Z date_updated: 2023-09-07T13:13:27Z day: '24' ddc: - '530' - '570' degree_awarded: PhD department: - _id: CaGu - _id: GaTk doi: 10.15479/AT:ISTA:8155 file: - access_level: open_access content_type: application/pdf creator: rgrah date_created: 2020-07-27T12:00:07Z date_updated: 2020-07-27T12:00:07Z file_id: '8176' file_name: Thesis_RokGrah_200727_convertedNew.pdf file_size: 16638998 relation: main_file success: 1 - access_level: closed content_type: application/zip creator: rgrah date_created: 2020-07-27T12:02:23Z date_updated: 2020-07-30T13:04:55Z file_id: '8177' file_name: Thesis_new.zip file_size: 347459978 relation: main_file file_date_updated: 2020-07-30T13:04:55Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '310' project: - _id: 267C84F4-B435-11E9-9278-68D0E5697425 name: Biophysically realistic genotype-phenotype maps for regulatory networks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7675' relation: part_of_dissertation status: public - id: '7569' relation: part_of_dissertation status: public - id: '7652' relation: part_of_dissertation status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Gene regulation across scales – how biophysical constraints shape evolution type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7643' acknowledgement: 'This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). ' article_processing_charge: No article_type: letter_note author: - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Hana full_name: Rakusova, Hana id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA last_name: Rakusova - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40. doi:10.1104/pp.20.00212 apa: Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212 chicago: Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212. ieee: H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” Plant Physiology, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020. ista: Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40. mla: Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212. short: H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40. date_created: 2020-04-06T10:06:40Z date_published: 2020-05-08T00:00:00Z date_updated: 2023-09-07T13:13:04Z day: '08' department: - _id: JiFr doi: 10.1104/pp.20.00212 ec_funded: 1 external_id: isi: - '000536641800018' pmid: - '32107280' intvolume: ' 183' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1104/pp.20.00212 month: '05' oa: 1 oa_version: Published Version page: 37-40 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' related_material: record: - id: '8589' relation: dissertation_contains status: public scopus_import: '1' status: public title: SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 183 year: '2020' ... --- _id: '7675' abstract: - lang: eng text: 'In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Benjamin full_name: Zoller, Benjamin last_name: Zoller - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405 apa: Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405 chicago: Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405. ieee: R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020. ista: Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405. mla: Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405. short: R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020). date_created: 2020-04-23T10:12:51Z date_published: 2020-04-09T00:00:00Z date_updated: 2023-09-07T13:13:26Z day: '09' department: - _id: CaGu - _id: GaTk doi: 10.1101/2020.04.08.029405 language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/2020.04.08.029405 ' month: '04' oa: 1 oa_version: Preprint project: - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? - _id: 267C84F4-B435-11E9-9278-68D0E5697425 name: Biophysically realistic genotype-phenotype maps for regulatory networks publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory related_material: record: - id: '8155' relation: dissertation_contains status: public status: public title: Normative models of enhancer function type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '7460' abstract: - lang: eng text: "Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Katharina full_name: Ölsböck, Katharina id: 4D4AA390-F248-11E8-B48F-1D18A9856A87 last_name: Ölsböck orcid: 0000-0002-4672-8297 citation: ama: Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460 apa: Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460 chicago: Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460. ieee: K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020. ista: Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria. mla: Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460. short: K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020. date_created: 2020-02-06T14:56:53Z date_published: 2020-02-10T00:00:00Z date_updated: 2023-09-07T13:15:30Z day: '10' ddc: - '514' degree_awarded: PhD department: - _id: HeEd - _id: GradSch doi: 10.15479/AT:ISTA:7460 file: - access_level: open_access checksum: 1df9f8c530b443c0e63a3f2e4fde412e content_type: application/pdf creator: koelsboe date_created: 2020-02-06T14:43:54Z date_updated: 2020-07-14T12:47:58Z file_id: '7461' file_name: thesis_ist-final_noack.pdf file_size: 76195184 relation: main_file - access_level: closed checksum: 7a52383c812b0be64d3826546509e5a4 content_type: application/x-zip-compressed creator: koelsboe date_created: 2020-02-06T14:52:45Z date_updated: 2020-07-14T12:47:58Z description: latex source files, figures file_id: '7462' file_name: latex-files.zip file_size: 122103715 relation: source_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' keyword: - shape reconstruction - hole manipulation - ordered complexes - Alpha complex - Wrap complex - computational topology - Bregman geometry language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '02' oa: 1 oa_version: Published Version page: '155' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6608' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: The hole system of triangulated shapes 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7896' abstract: - lang: eng text: "A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg citation: ama: Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896 apa: Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896 chicago: Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896. ieee: C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020. ista: Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria. mla: Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896. short: C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020. date_created: 2020-05-26T14:08:55Z date_published: 2020-05-25T00:00:00Z date_updated: 2023-09-07T13:15:55Z day: '25' ddc: - '000' degree_awarded: PhD department: - _id: KrPi doi: 10.15479/AT:ISTA:7896 ec_funded: 1 file: - access_level: open_access checksum: b39e2e1c376f5819b823fb7077491c64 content_type: application/pdf creator: dernst date_created: 2020-05-26T14:08:13Z date_updated: 2020-07-14T12:48:04Z file_id: '7897' file_name: 2020_Thesis_Kamath.pdf file_size: 1622742 relation: main_file - access_level: closed checksum: 8b26ba729c1a85ac6bea775f5d73cdc7 content_type: application/x-zip-compressed creator: dernst date_created: 2020-05-26T14:08:23Z date_updated: 2020-07-14T12:48:04Z file_id: '7898' file_name: Thesis_Kamath.zip file_size: 15301529 relation: source_file file_date_updated: 2020-07-14T12:48:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '126' project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6677' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: On the average-case hardness of total search problems 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7936' abstract: - lang: eng text: 'State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures.' article_number: 1716-1725 article_processing_charge: No author: - first_name: Amélie full_name: Royer, Amélie id: 3811D890-F248-11E8-B48F-1D18A9856A87 last_name: Royer orcid: 0000-0002-8407-0705 - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093288' apa: 'Royer, A., & Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093288' chicago: Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093288. ieee: A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020. ista: 'Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.' mla: Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” IEEE Winter Conference on Applications of Computer Vision, 1716–1725, IEEE, 2020, doi:10.1109/WACV45572.2020.9093288. short: A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020. conference: end_date: 2020-03-05 location: ' Snowmass Village, CO, United States' name: 'WACV: Winter Conference on Applications of Computer Vision' start_date: 2020-03-01 date_created: 2020-06-07T22:00:53Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-07T13:16:17Z day: '01' department: - _id: ChLa doi: 10.1109/WACV45572.2020.9093288 external_id: arxiv: - '2004.12623' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2004.12623 month: '03' oa: 1 oa_version: Preprint publication: IEEE Winter Conference on Applications of Computer Vision publication_identifier: isbn: - '9781728165530' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '8331' relation: dissertation_contains status: deleted - id: '8390' relation: dissertation_contains status: public scopus_import: 1 status: public title: Localizing grouped instances for efficient detection in low-resource scenarios type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '7937' abstract: - lang: eng text: 'Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning.' article_number: 2180-2189 article_processing_charge: No author: - first_name: Amélie full_name: Royer, Amélie id: 3811D890-F248-11E8-B48F-1D18A9856A87 last_name: Royer orcid: 0000-0002-8407-0705 - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093635' apa: 'Royer, A., & Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In 2020 IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093635' chicago: Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093635. ieee: A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in 2020 IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020. ista: 'Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189.' mla: Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” 2020 IEEE Winter Conference on Applications of Computer Vision, 2180–2189, IEEE, 2020, doi:10.1109/WACV45572.2020.9093635. short: A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020. conference: end_date: 2020-03-05 location: Snowmass Village, CO, United States name: 'WACV: Winter Conference on Applications of Computer Vision' start_date: 2020-03-01 date_created: 2020-06-07T22:00:53Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-07T13:16:17Z day: '01' department: - _id: ChLa doi: 10.1109/WACV45572.2020.9093635 external_id: arxiv: - '2008.11995' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/2008.11995 month: '03' oa: 1 oa_version: Preprint publication: 2020 IEEE Winter Conference on Applications of Computer Vision publication_identifier: isbn: - '9781728165530' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '8331' relation: dissertation_contains status: deleted - id: '8390' relation: dissertation_contains status: public scopus_import: '1' status: public title: A flexible selection scheme for minimum-effort transfer learning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8193' abstract: - lang: eng text: 'Multiple-environment Markov decision processes (MEMDPs) are MDPs equipped with not one, but multiple probabilistic transition functions, which represent the various possible unknown environments. While the previous research on MEMDPs focused on theoretical properties for long-run average payoff, we study them with discounted-sum payoff and focus on their practical advantages and applications. MEMDPs can be viewed as a special case of Partially observable and Mixed observability MDPs: the state of the system is perfectly observable, but not the environment. We show that the specific structure of MEMDPs allows for more efficient algorithmic analysis, in particular for faster belief updates. We demonstrate the applicability of MEMDPs in several domains. In particular, we formalize the sequential decision-making approach to contextual recommendation systems as MEMDPs and substantially improve over the previous MDP approach.' acknowledgement: Krishnendu Chatterjee is supported by the Austrian ScienceFund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE),and COST Action GAMENET. Petr Novotn ́y is supported bythe Czech Science Foundation grant No. GJ19-15134Y. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Deep full_name: Karkhanis, Deep last_name: Karkhanis - first_name: Petr full_name: Novotný, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotný - first_name: Amélie full_name: Royer, Amélie id: 3811D890-F248-11E8-B48F-1D18A9856A87 last_name: Royer orcid: 0000-0002-8407-0705 citation: ama: 'Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. Multiple-environment Markov decision processes: Efficient analysis and applications. In: Proceedings of the 30th International Conference on Automated Planning and Scheduling. Vol 30. Association for the Advancement of Artificial Intelligence; 2020:48-56.' apa: 'Chatterjee, K., Chmelik, M., Karkhanis, D., Novotný, P., & Royer, A. (2020). Multiple-environment Markov decision processes: Efficient analysis and applications. In Proceedings of the 30th International Conference on Automated Planning and Scheduling (Vol. 30, pp. 48–56). Nancy, France: Association for the Advancement of Artificial Intelligence.' chicago: 'Chatterjee, Krishnendu, Martin Chmelik, Deep Karkhanis, Petr Novotný, and Amélie Royer. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” In Proceedings of the 30th International Conference on Automated Planning and Scheduling, 30:48–56. Association for the Advancement of Artificial Intelligence, 2020.' ieee: 'K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, and A. Royer, “Multiple-environment Markov decision processes: Efficient analysis and applications,” in Proceedings of the 30th International Conference on Automated Planning and Scheduling, Nancy, France, 2020, vol. 30, pp. 48–56.' ista: 'Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. 2020. Multiple-environment Markov decision processes: Efficient analysis and applications. Proceedings of the 30th International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 30, 48–56.' mla: 'Chatterjee, Krishnendu, et al. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” Proceedings of the 30th International Conference on Automated Planning and Scheduling, vol. 30, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.' short: K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, A. Royer, in:, Proceedings of the 30th International Conference on Automated Planning and Scheduling, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56. conference: end_date: 2020-10-30 location: Nancy, France name: 'ICAPS: International Conference on Automated Planning and Scheduling' start_date: 2020-10-26 date_created: 2020-08-02T22:00:58Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-09-07T13:16:18Z day: '01' department: - _id: KrCh intvolume: ' 30' language: - iso: eng month: '06' oa_version: None page: 48-56 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Proceedings of the 30th International Conference on Automated Planning and Scheduling publication_identifier: eissn: - '23340843' issn: - '23340835' publication_status: published publisher: Association for the Advancement of Artificial Intelligence quality_controlled: '1' related_material: record: - id: '8390' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Multiple-environment Markov decision processes: Efficient analysis and applications' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2020' ... --- _id: '8092' abstract: - lang: eng text: Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html. article_processing_charge: No author: - first_name: Amélie full_name: Royer, Amélie id: 3811D890-F248-11E8-B48F-1D18A9856A87 last_name: Royer orcid: 0000-0002-8407-0705 - first_name: Konstantinos full_name: Bousmalis, Konstantinos last_name: Bousmalis - first_name: Stephan full_name: Gouws, Stephan last_name: Gouws - first_name: Fred full_name: Bertsch, Fred last_name: Bertsch - first_name: Inbar full_name: Mosseri, Inbar last_name: Mosseri - first_name: Forrester full_name: Cole, Forrester last_name: Cole - first_name: Kevin full_name: Murphy, Kevin last_name: Murphy citation: ama: 'Royer A, Bousmalis K, Gouws S, et al. XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Singh R, Vatsa M, Patel VM, Ratha N, eds. Domain Adaptation for Visual Understanding. Springer Nature; 2020:33-49. doi:10.1007/978-3-030-30671-7_3' apa: 'Royer, A., Bousmalis, K., Gouws, S., Bertsch, F., Mosseri, I., Cole, F., & Murphy, K. (2020). XGAN: Unsupervised image-to-image translation for many-to-many mappings. In R. Singh, M. Vatsa, V. M. Patel, & N. Ratha (Eds.), Domain Adaptation for Visual Understanding (pp. 33–49). Springer Nature. https://doi.org/10.1007/978-3-030-30671-7_3' chicago: 'Royer, Amélie, Konstantinos Bousmalis, Stephan Gouws, Fred Bertsch, Inbar Mosseri, Forrester Cole, and Kevin Murphy. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” In Domain Adaptation for Visual Understanding, edited by Richa Singh, Mayank Vatsa, Vishal M. Patel, and Nalini Ratha, 33–49. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-30671-7_3.' ieee: 'A. Royer et al., “XGAN: Unsupervised image-to-image translation for many-to-many mappings,” in Domain Adaptation for Visual Understanding, R. Singh, M. Vatsa, V. M. Patel, and N. Ratha, Eds. Springer Nature, 2020, pp. 33–49.' ista: 'Royer A, Bousmalis K, Gouws S, Bertsch F, Mosseri I, Cole F, Murphy K. 2020.XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Domain Adaptation for Visual Understanding. , 33–49.' mla: 'Royer, Amélie, et al. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” Domain Adaptation for Visual Understanding, edited by Richa Singh et al., Springer Nature, 2020, pp. 33–49, doi:10.1007/978-3-030-30671-7_3.' short: A. Royer, K. Bousmalis, S. Gouws, F. Bertsch, I. Mosseri, F. Cole, K. Murphy, in:, R. Singh, M. Vatsa, V.M. Patel, N. Ratha (Eds.), Domain Adaptation for Visual Understanding, Springer Nature, 2020, pp. 33–49. date_created: 2020-07-05T22:00:46Z date_published: 2020-01-08T00:00:00Z date_updated: 2023-09-07T13:16:18Z day: '08' department: - _id: ChLa doi: 10.1007/978-3-030-30671-7_3 editor: - first_name: Richa full_name: Singh, Richa last_name: Singh - first_name: Mayank full_name: Vatsa, Mayank last_name: Vatsa - first_name: Vishal M. full_name: Patel, Vishal M. last_name: Patel - first_name: Nalini full_name: Ratha, Nalini last_name: Ratha external_id: arxiv: - '1711.05139' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.05139 month: '01' oa: 1 oa_version: Preprint page: 33-49 publication: Domain Adaptation for Visual Understanding publication_identifier: isbn: - '9783030306717' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8331' relation: dissertation_contains status: deleted - id: '8390' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'XGAN: Unsupervised image-to-image translation for many-to-many mappings' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '7944' abstract: - lang: eng text: "This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 citation: ama: Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944 apa: Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944 chicago: Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944. ieee: Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020. ista: Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria. mla: Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944. short: Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020. date_created: 2020-06-08T00:49:46Z date_published: 2020-06-09T00:00:00Z date_updated: 2023-09-07T13:17:37Z day: '09' ddc: - '516' - '514' degree_awarded: PhD department: - _id: HeEd - _id: UlWa doi: 10.15479/AT:ISTA:7944 file: - access_level: open_access checksum: df688bc5a82b50baee0b99d25fc7b7f0 content_type: application/pdf creator: zmasarov date_created: 2020-06-08T00:34:00Z date_updated: 2020-07-14T12:48:05Z file_id: '7945' file_name: THESIS_Zuzka_Masarova.pdf file_size: 13661779 relation: main_file - access_level: closed checksum: 45341a35b8f5529c74010b7af43ac188 content_type: application/zip creator: zmasarov date_created: 2020-06-08T00:35:30Z date_updated: 2020-07-14T12:48:05Z file_id: '7946' file_name: THESIS_Zuzka_Masarova_SOURCE_FILES.zip file_size: 32184006 relation: source_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' keyword: - reconfiguration - reconfiguration graph - triangulations - flip - constrained triangulations - shellability - piecewise-linear balls - token swapping - trees - coloured weighted token swapping language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '06' oa: 1 oa_version: Published Version page: '160' publication_identifier: isbn: - 978-3-99078-005-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7950' relation: part_of_dissertation status: public - id: '5986' relation: part_of_dissertation status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Reconfiguration problems tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8587' abstract: - lang: eng text: Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules. acknowledgement: We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868. article_number: '164302' article_processing_charge: No article_type: original author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Richard full_name: Schmidt, Richard last_name: Schmidt - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 citation: ama: Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 2020;152(16). doi:10.1063/1.5144759 apa: Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., & Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5144759 chicago: Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/1.5144759. ieee: X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” The Journal of Chemical Physics, vol. 152, no. 16. AIP Publishing, 2020. ista: Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302. mla: Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:10.1063/1.5144759. short: X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020). date_created: 2020-09-30T10:33:17Z date_published: 2020-04-27T00:00:00Z date_updated: 2023-09-07T13:16:42Z day: '27' department: - _id: MiLe - _id: RoSe doi: 10.1063/1.5144759 ec_funded: 1 external_id: arxiv: - '1912.02658' isi: - '000530448300001' intvolume: ' 152' isi: 1 issue: '16' keyword: - Physical and Theoretical Chemistry - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.02658 month: '04' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: record: - id: '8958' relation: dissertation_contains status: public status: public title: Intermolecular forces and correlations mediated by a phonon bath type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 152 year: '2020' ... --- _id: '8341' abstract: - lang: eng text: "One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: NanoFab acknowledgement: My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Urban full_name: Bezeljak, Urban id: 2A58201A-F248-11E8-B48F-1D18A9856A87 last_name: Bezeljak orcid: 0000-0003-1365-5631 citation: ama: Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341 apa: Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341 chicago: Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341. ieee: U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020. ista: Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. mla: Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341. short: U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020. date_created: 2020-09-08T08:53:53Z date_published: 2020-09-08T00:00:00Z date_updated: 2023-09-07T13:17:06Z day: '08' ddc: - '570' degree_awarded: PhD department: - _id: MaLo doi: 10.15479/AT:ISTA:8341 file: - access_level: closed checksum: 70871b335a595252a66c6bbf0824fb02 content_type: application/x-zip-compressed creator: dernst date_created: 2020-09-08T09:00:29Z date_updated: 2021-09-16T12:49:12Z file_id: '8342' file_name: 2020_Urban_Bezeljak_Thesis_TeX.zip file_size: 65246782 relation: source_file - access_level: open_access checksum: 59a62275088b00b7241e6ff4136434c7 content_type: application/pdf creator: dernst date_created: 2020-09-08T09:00:27Z date_updated: 2021-09-16T12:49:12Z file_id: '8343' file_name: 2020_Urban_Bezeljak_Thesis.pdf file_size: 31259058 relation: main_file file_date_updated: 2021-09-16T12:49:12Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '215' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7580' relation: part_of_dissertation status: public status: public supervisor: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: In vitro reconstitution of a Rab activation switch 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7580' abstract: - lang: eng text: The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell. acknowledged_ssus: - _id: Bio - _id: LifeSc article_processing_charge: No article_type: original author: - first_name: Urban full_name: Bezeljak, Urban id: 2A58201A-F248-11E8-B48F-1D18A9856A87 last_name: Bezeljak orcid: 0000-0003-1365-5631 - first_name: Hrushikesh full_name: Loya, Hrushikesh last_name: Loya - first_name: Beata M full_name: Kaczmarek, Beata M id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarek - first_name: Timothy E. full_name: Saunders, Timothy E. last_name: Saunders - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117 apa: Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117 chicago: Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117. ieee: U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” Proceedings of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020. ista: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549. mla: Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:10.1073/pnas.1921027117. short: U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549. date_created: 2020-03-12T05:32:26Z date_published: 2020-03-24T00:00:00Z date_updated: 2023-09-07T13:17:06Z day: '24' department: - _id: MaLo - _id: CaBe doi: 10.1073/pnas.1921027117 external_id: isi: - '000521821800040' intvolume: ' 117' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/776567 month: '03' oa: 1 oa_version: Preprint page: 6504-6549 project: - _id: 2599F062-B435-11E9-9278-68D0E5697425 grant_number: RGY0083/2016 name: Reconstitution of cell polarity and axis determination in a cell-free system publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/proteins-as-molecular-switches/ record: - id: '8341' relation: dissertation_contains status: public scopus_import: '1' status: public title: Stochastic activation and bistability in a Rab GTPase regulatory network type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 117 year: '2020' ... --- _id: '8032' abstract: - lang: eng text: "Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus." acknowledged_ssus: - _id: E-Lib - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kristóf full_name: Huszár, Kristóf id: 33C26278-F248-11E8-B48F-1D18A9856A87 last_name: Huszár orcid: 0000-0002-5445-5057 citation: ama: Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032 apa: Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032 chicago: Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032. ieee: K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020. ista: Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. mla: Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032. short: K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020. date_created: 2020-06-26T10:00:36Z date_published: 2020-06-26T00:00:00Z date_updated: 2023-09-07T13:18:27Z day: '26' ddc: - '514' degree_awarded: PhD department: - _id: UlWa doi: 10.15479/AT:ISTA:8032 file: - access_level: open_access checksum: bd8be6e4f1addc863dfcc0fad29ee9c3 content_type: application/pdf creator: khuszar date_created: 2020-06-26T10:03:58Z date_updated: 2020-07-14T12:48:08Z file_id: '8034' file_name: Kristof_Huszar-Thesis.pdf file_size: 2637562 relation: main_file - access_level: closed checksum: d5f8456202b32f4a77552ef47a2837d1 content_type: application/x-zip-compressed creator: khuszar date_created: 2020-06-26T10:10:06Z date_updated: 2020-07-14T12:48:08Z file_id: '8035' file_name: Kristof_Huszar-Thesis-source.zip file_size: 7163491 relation: source_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: xviii+120 publication_identifier: isbn: - 978-3-99078-006-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6556' relation: dissertation_contains status: public - id: '7093' relation: dissertation_contains status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Jonathan full_name: Spreer, Jonathan last_name: Spreer title: Combinatorial width parameters for 3-dimensional manifolds 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8195' abstract: - lang: eng text: This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier. acknowledgement: "Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award)." alternative_title: - LNCS article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: Computer Aided Verification. Vol 12224. Springer Nature; 2020:275-298. doi:10.1007/978-3-030-53288-8_14' apa: Kragl, B., Qadeer, S., & Henzinger, T. A. (2020). Refinement for structured concurrent programs. In Computer Aided Verification (Vol. 12224, pp. 275–298). Springer Nature. https://doi.org/10.1007/978-3-030-53288-8_14 chicago: Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In Computer Aided Verification, 12224:275–98. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53288-8_14. ieee: B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in Computer Aided Verification, 2020, vol. 12224, pp. 275–298. ista: Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298. mla: Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” Computer Aided Verification, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:10.1007/978-3-030-53288-8_14. short: B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298. date_created: 2020-08-03T11:45:35Z date_published: 2020-07-14T00:00:00Z date_updated: 2023-09-07T13:18:00Z day: '14' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-53288-8_14 external_id: isi: - '000695276000014' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-06T08:14:54Z date_updated: 2020-08-06T08:14:54Z file_id: '8201' file_name: 2020_LNCS_Kragl.pdf file_size: 804237 relation: main_file success: 1 file_date_updated: 2020-08-06T08:14:54Z has_accepted_license: '1' intvolume: ' 12224' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 275-298 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Computer Aided Verification publication_identifier: eisbn: - '9783030532888' eissn: - 1611-3349 isbn: - '9783030532871' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8332' relation: dissertation_contains status: public scopus_import: '1' status: public title: Refinement for structured concurrent programs 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12224 year: '2020' ... --- _id: '8012' abstract: - lang: eng text: Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos. article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Constantin full_name: Enea, Constantin last_name: Enea - 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: Suha Orhun full_name: Mutluergil, Suha Orhun last_name: Mutluergil - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: 'Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. Inductive sequentialization of asynchronous programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:227-242. doi:10.1145/3385412.3385980' apa: 'Kragl, B., Enea, C., Henzinger, T. A., Mutluergil, S. O., & Qadeer, S. (2020). Inductive sequentialization of asynchronous programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 227–242). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385980' chicago: Kragl, Bernhard, Constantin Enea, Thomas A Henzinger, Suha Orhun Mutluergil, and Shaz Qadeer. “Inductive Sequentialization of Asynchronous Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 227–42. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385980. ieee: B. Kragl, C. Enea, T. A. Henzinger, S. O. Mutluergil, and S. Qadeer, “Inductive sequentialization of asynchronous programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 227–242. ista: 'Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. 2020. Inductive sequentialization of asynchronous programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 227–242.' mla: Kragl, Bernhard, et al. “Inductive Sequentialization of Asynchronous Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–42, doi:10.1145/3385412.3385980. short: B. Kragl, C. Enea, T.A. Henzinger, S.O. Mutluergil, S. Qadeer, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–242. conference: end_date: 2020-06-20 location: London, United Kingdom name: 'PLDI: Programming Language Design and Implementation' start_date: 2020-06-15 date_created: 2020-06-25T11:40:16Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-09-07T13:18:00Z day: '01' department: - _id: ToHe doi: 10.1145/3385412.3385980 external_id: isi: - '000614622300016' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3385412.3385980 month: '06' oa: 1 oa_version: Published Version page: 227-242 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation publication_identifier: isbn: - '9781450376136' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '8332' relation: dissertation_contains status: public scopus_import: '1' status: public title: Inductive sequentialization of asynchronous programs type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '8358' abstract: - lang: eng text: "During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n" acknowledged_ssus: - _id: Bio acknowledgement: I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Paulo R full_name: Dos Santos Caldas, Paulo R id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87 last_name: Dos Santos Caldas orcid: 0000-0001-6730-4461 citation: ama: Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358 apa: Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358 chicago: Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358. ieee: P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020. ista: Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. mla: Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358. short: P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020. date_created: 2020-09-10T09:26:49Z date_published: 2020-09-10T00:00:00Z date_updated: 2023-09-07T13:18:51Z day: '10' ddc: - '572' degree_awarded: PhD department: - _id: MaLo doi: 10.15479/AT:ISTA:8358 file: - access_level: open_access checksum: 882f93fe9c351962120e2669b84bf088 content_type: application/pdf creator: pcaldas date_created: 2020-09-10T12:11:29Z date_updated: 2020-09-10T12:11:29Z file_id: '8364' file_name: phd_thesis_pcaldas.pdf file_size: 141602462 relation: main_file success: 1 - access_level: closed checksum: 70cc9e399c4e41e6e6ac445ae55e8558 content_type: application/x-zip-compressed creator: pcaldas date_created: 2020-09-10T12:18:17Z date_updated: 2020-09-11T07:48:10Z file_id: '8365' file_name: phd_thesis_latex_pcaldas.zip file_size: 450437458 relation: source_file file_date_updated: 2020-09-11T07:48:10Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '135' publication_identifier: isbn: - 978-3-99078-009-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7572' relation: dissertation_contains status: public - id: '7197' relation: part_of_dissertation status: public status: public supervisor: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8703' abstract: - lang: eng text: 'Even though Delaunay originally introduced his famous triangulations in the case of infinite point sets with translational periodicity, a software that computes such triangulations in the general case is not yet available, to the best of our knowledge. Combining and generalizing previous work, we present a practical algorithm for computing such triangulations. The algorithm has been implemented and experiments show that its performance is as good as the one of the CGAL package, which is restricted to cubic periodicity. ' alternative_title: - LIPIcs article_number: '75' article_processing_charge: No author: - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 - first_name: Mael full_name: Rouxel-Labbé, Mael last_name: Rouxel-Labbé - first_name: Monique full_name: Teillaud, Monique last_name: Teillaud citation: ama: 'Osang GF, Rouxel-Labbé M, Teillaud M. Generalizing CGAL periodic Delaunay triangulations. In: 28th Annual European Symposium on Algorithms. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.75' apa: 'Osang, G. F., Rouxel-Labbé, M., & Teillaud, M. (2020). Generalizing CGAL periodic Delaunay triangulations. In 28th Annual European Symposium on Algorithms (Vol. 173). Virtual, Online; Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.75' chicago: Osang, Georg F, Mael Rouxel-Labbé, and Monique Teillaud. “Generalizing CGAL Periodic Delaunay Triangulations.” In 28th Annual European Symposium on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ESA.2020.75. ieee: G. F. Osang, M. Rouxel-Labbé, and M. Teillaud, “Generalizing CGAL periodic Delaunay triangulations,” in 28th Annual European Symposium on Algorithms, Virtual, Online; Pisa, Italy, 2020, vol. 173. ista: 'Osang GF, Rouxel-Labbé M, Teillaud M. 2020. Generalizing CGAL periodic Delaunay triangulations. 28th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 75.' mla: Osang, Georg F., et al. “Generalizing CGAL Periodic Delaunay Triangulations.” 28th Annual European Symposium on Algorithms, vol. 173, 75, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.75. short: G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. conference: end_date: 2020-09-09 location: Virtual, Online; Pisa, Italy name: 'ESA: Annual European Symposium on Algorithms' start_date: 2020-09-07 date_created: 2020-10-25T23:01:18Z date_published: 2020-08-26T00:00:00Z date_updated: 2023-09-07T13:29:00Z day: '26' ddc: - '000' department: - _id: HeEd doi: 10.4230/LIPIcs.ESA.2020.75 ec_funded: 1 file: - access_level: open_access checksum: fe0f7c49a99ed870c671b911e10d5496 content_type: application/pdf creator: cziletti date_created: 2020-10-27T14:31:52Z date_updated: 2020-10-27T14:31:52Z file_id: '8712' file_name: 2020_LIPIcs_Osang.pdf file_size: 733291 relation: main_file success: 1 file_date_updated: 2020-10-27T14:31:52Z has_accepted_license: '1' intvolume: ' 173' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '08' oa: 1 oa_version: Published Version project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended publication: 28th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959771627' issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '9056' relation: dissertation_contains status: public scopus_import: '1' status: public title: Generalizing CGAL periodic Delaunay triangulations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 173 year: '2020' ... --- _id: '7481' abstract: - lang: eng text: 'We address the following question: How redundant is the parameterisation of ReLU networks? Specifically, we consider transformations of the weight space which leave the function implemented by the network intact. Two such transformations are known for feed-forward architectures: permutation of neurons within a layer, and positive scaling of all incoming weights of a neuron coupled with inverse scaling of its outgoing weights. In this work, we show for architectures with non-increasing widths that permutation and scaling are in fact the only function-preserving weight transformations. For any eligible architecture we give an explicit construction of a neural network such that any other network that implements the same function can be obtained from the original one by the application of permutations and rescaling. The proof relies on a geometric understanding of boundaries between linear regions of ReLU networks, and we hope the developed mathematical tools are of independent interest.' article_processing_charge: No author: - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: 8th International Conference on Learning Representations. ; 2020.' apa: Phuong, M., & Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In 8th International Conference on Learning Representations. Online. chicago: Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020. ieee: M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020. ista: 'Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020. short: M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020. conference: end_date: 2020-04-30 location: Online name: 'ICLR: International Conference on Learning Representations' start_date: 2020-04-27 date_created: 2020-02-11T09:07:37Z date_published: 2020-04-26T00:00:00Z date_updated: 2023-09-07T13:29:50Z day: '26' ddc: - '000' department: - _id: ChLa file: - access_level: open_access checksum: 8d372ea5defd8cb8fdc430111ed754a9 content_type: application/pdf creator: bphuong date_created: 2020-02-11T09:07:27Z date_updated: 2020-07-14T12:47:59Z file_id: '7482' file_name: main.pdf file_size: 405469 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: 8th International Conference on Learning Representations publication_status: published quality_controlled: '1' related_material: link: - relation: supplementary_material url: https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html record: - id: '9418' relation: dissertation_contains status: public status: public title: Functional vs. parametric equivalence of ReLU networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9781' abstract: - lang: eng text: We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum. acknowledgement: We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227. article_processing_charge: No article_type: original author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 2020;52(1):605-622. doi:10.1137/19m126284x apa: Feliciangeli, D., & Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics . https://doi.org/10.1137/19m126284x chicago: Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics , 2020. https://doi.org/10.1137/19m126284x. ieee: D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” SIAM Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial & Applied Mathematics , pp. 605–622, 2020. ista: Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622. mla: Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis, vol. 52, no. 1, Society for Industrial & Applied Mathematics , 2020, pp. 605–22, doi:10.1137/19m126284x. short: D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622. date_created: 2021-08-06T07:34:16Z date_published: 2020-02-12T00:00:00Z date_updated: 2023-09-07T13:30:11Z day: '12' ddc: - '510' department: - _id: RoSe doi: 10.1137/19m126284x ec_funded: 1 external_id: arxiv: - '1904.08647 ' isi: - '000546967700022' has_accepted_license: '1' intvolume: ' 52' isi: 1 issue: '1' keyword: - Applied Mathematics - Computational Mathematics - Analysis language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://arxiv.org/abs/1904.08647 month: '02' oa: 1 oa_version: Preprint page: 605-622 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - 1095-7154 issn: - 0036-1410 publication_status: published publisher: 'Society for Industrial & Applied Mathematics ' quality_controlled: '1' related_material: record: - id: '9733' relation: dissertation_contains status: public scopus_import: '1' status: public title: Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2020' ... --- _id: '7489' abstract: - lang: eng text: 'In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 citation: ama: Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 2020;236:967-1087. doi:10.1007/s00205-019-01486-2 apa: Fischer, J. L., & Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01486-2 chicago: Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-019-01486-2. ieee: J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” Archive for Rational Mechanics and Analysis, vol. 236. Springer Nature, pp. 967–1087, 2020. ista: Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087. mla: Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:10.1007/s00205-019-01486-2. short: J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087. date_created: 2020-02-16T23:00:50Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-09-07T13:30:45Z day: '01' ddc: - '530' - '532' department: - _id: JuFi doi: 10.1007/s00205-019-01486-2 ec_funded: 1 external_id: isi: - '000511060200001' file: - access_level: open_access checksum: f107e21b58f5930876f47144be37cf6c content_type: application/pdf creator: dernst date_created: 2020-11-20T09:14:22Z date_updated: 2020-11-20T09:14:22Z file_id: '8779' file_name: 2020_ArchRatMechAn_Fischer.pdf file_size: 1897571 relation: main_file success: 1 file_date_updated: 2020-11-20T09:14:22Z has_accepted_license: '1' intvolume: ' 236' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 967-1087 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - '14320673' issn: - '00039527' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10007' relation: dissertation_contains status: public scopus_import: '1' status: public title: Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 236 year: '2020' ... --- _id: '10012' abstract: - lang: eng text: We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a "gradient flow calibration" ensures that the route of steepest descent in the energy landscape is unique and stable. acknowledgement: Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385. article_number: '2003.05478' article_processing_charge: No author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 - first_name: Tim full_name: Laux, Tim last_name: Laux - first_name: Thilo full_name: Simon, Thilo last_name: Simon citation: ama: 'Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.' apa: 'Fischer, J. L., Hensel, S., Laux, T., & Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.' chicago: 'Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, n.d.' ieee: 'J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” arXiv. .' ista: 'Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.' mla: 'Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, 2003.05478.' short: J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.). date_created: 2021-09-13T12:17:11Z date_published: 2020-03-11T00:00:00Z date_updated: 2023-09-07T13:30:45Z day: '11' department: - _id: JuFi ec_funded: 1 external_id: arxiv: - '2003.05478' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2003.05478 month: '03' oa: 1 oa_version: Preprint project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: arXiv publication_status: submitted related_material: record: - id: '10007' relation: dissertation_contains status: public status: public title: 'The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8755' abstract: - lang: eng text: 'The superconducting circuit community has recently discovered the promising potential of superinductors. These circuit elements have a characteristic impedance exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of ground state charge fluctuations. Applications include the realization of hardware protected qubits for fault tolerant quantum computing, improved coupling to small dipole moment objects and defining a new quantum metrology standard for the ampere. In this work we refute the widespread notion that superinductors can only be implemented based on kinetic inductance, i.e. using disordered superconductors or Josephson junction arrays. We present modeling, fabrication and characterization of 104 planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled tunneling events and offer high reproducibility, linearity and the ability to couple magnetically - properties that significantly broaden the scope of future quantum circuits. ' acknowledged_ssus: - _id: NanoFab acknowledgement: "The authors acknowledge the support from I. Prieto and the IST Nanofabrication Facility. This work was supported by IST Austria and a NOMIS foundation research grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European Union’s Horizon 2020 research and innovation programs under grant agreement No 732894 (FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). " article_number: '044055' article_processing_charge: No article_type: original author: - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - 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: Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 2020;14(4). doi:10.1103/PhysRevApplied.14.044055 apa: Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.14.044055 chicago: Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied. American Physical Society, 2020. https://doi.org/10.1103/PhysRevApplied.14.044055. ieee: M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor,” Physical Review Applied, vol. 14, no. 4. American Physical Society, 2020. ista: Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055. mla: Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied, vol. 14, no. 4, 044055, American Physical Society, 2020, doi:10.1103/PhysRevApplied.14.044055. short: M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020). date_created: 2020-11-15T23:01:17Z date_published: 2020-10-29T00:00:00Z date_updated: 2023-09-07T13:31:22Z day: '29' ddc: - '530' department: - _id: JoFi doi: 10.1103/PhysRevApplied.14.044055 ec_funded: 1 external_id: arxiv: - '2007.01644' isi: - '000582797300003' file: - access_level: open_access checksum: 2a634abe75251ae7628cd54c8a4ce2e8 content_type: application/pdf creator: dernst date_created: 2021-03-29T11:43:20Z date_updated: 2021-03-29T11:43:20Z file_id: '9300' file_name: 2020_PhysReviewApplied_Peruzzo.pdf file_size: 2607823 relation: main_file success: 1 file_date_updated: 2021-03-29T11:43:20Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits publication: Physical Review Applied publication_identifier: eissn: - '23317019' publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '13070' relation: research_data status: public - id: '9920' relation: dissertation_contains status: public scopus_import: '1' status: public title: Surpassing the resistance quantum with a geometric superinductor type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2020' ... --- _id: '7573' abstract: - lang: eng text: This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport. acknowledgement: J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276. article_processing_charge: No article_type: original author: - first_name: Peter full_name: Gladbach, Peter last_name: Gladbach - first_name: Eva full_name: Kopfer, Eva last_name: Kopfer - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 2020;139(7):204-234. doi:10.1016/j.matpur.2020.02.008 apa: Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. Elsevier. https://doi.org/10.1016/j.matpur.2020.02.008 chicago: Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees. Elsevier, 2020. https://doi.org/10.1016/j.matpur.2020.02.008. ieee: P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7. Elsevier, pp. 204–234, 2020. ista: Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234. mla: Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:10.1016/j.matpur.2020.02.008. short: P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234. date_created: 2020-03-08T23:00:47Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-09-07T13:31:05Z day: '01' department: - _id: JaMa doi: 10.1016/j.matpur.2020.02.008 ec_funded: 1 external_id: arxiv: - '1905.05757' isi: - '000539439400008' intvolume: ' 139' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.05757 month: '07' oa: 1 oa_version: Preprint page: 204-234 project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: ' F06504' name: Taming Complexity in Partial Di erential Systems - _id: 260788DE-B435-11E9-9278-68D0E5697425 call_identifier: FWF name: Dissipation and Dispersion in Nonlinear Partial Differential Equations publication: Journal de Mathematiques Pures et Appliquees publication_identifier: issn: - '00217824' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '10030' relation: dissertation_contains status: public scopus_import: '1' status: public title: Homogenisation of one-dimensional discrete optimal transport type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 139 year: '2020' ... --- _id: '10022' abstract: - lang: eng text: We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality. acknowledgement: This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245. article_number: '2008.10962' article_processing_charge: No author: - first_name: Dominik L full_name: Forkert, Dominik L id: 35C79D68-F248-11E8-B48F-1D18A9856A87 last_name: Forkert - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv. apa: Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv. chicago: Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, n.d. ieee: D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” arXiv. . ista: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962. mla: Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962. short: D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.). date_created: 2021-09-17T10:57:27Z date_published: 2020-08-25T00:00:00Z date_updated: 2023-09-07T13:31:05Z day: '25' department: - _id: JaMa ec_funded: 1 external_id: arxiv: - '2008.10962' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.10962 month: '08' oa: 1 oa_version: Preprint page: '33' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: submitted related_material: record: - id: '11739' relation: later_version status: public - id: '10030' relation: dissertation_contains status: public status: public title: Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8724' abstract: - lang: eng text: "We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. " acknowledged_ssus: - _id: ScienComp acknowledgement: Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). article_processing_charge: No author: - first_name: Nikola H full_name: Konstantinov, Nikola H id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87 last_name: Konstantinov - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.' apa: 'Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425). Online: ML Research Press.' chicago: Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In Proceedings of the 37th International Conference on Machine Learning, 119:5416–25. ML Research Press, 2020. ieee: N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in Proceedings of the 37th International Conference on Machine Learning, Online, 2020, vol. 119, pp. 5416–5425. ista: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.' mla: Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 5416–25. short: N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425. conference: end_date: 2020-07-18 location: Online name: 'ICML: International Conference on Machine Learning' start_date: 2020-07-12 date_created: 2020-11-05T15:25:58Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-09-07T13:42:08Z day: '12' ddc: - '000' department: - _id: DaAl - _id: ChLa ec_funded: 1 external_id: arxiv: - '2002.10384' file: - access_level: open_access checksum: cc755d0054bc4b2be778ea7aa7884d2f content_type: application/pdf creator: dernst date_created: 2021-02-15T09:00:01Z date_updated: 2021-02-15T09:00:01Z file_id: '9120' file_name: 2020_PMLR_Konstantinov.pdf file_size: 281286 relation: main_file success: 1 file_date_updated: 2021-02-15T09:00:01Z has_accepted_license: '1' intvolume: ' 119' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 5416-5425 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 37th International Conference on Machine Learning publication_identifier: issn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: supplementary_material url: http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf record: - id: '10799' relation: dissertation_contains status: public scopus_import: '1' status: public title: On the sample complexity of adversarial multi-source PAC learning type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '8644' abstract: - lang: eng text: Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures. acknowledgement: We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster). article_number: '093026' article_processing_charge: No article_type: original author: - first_name: Wojciech full_name: Rzadkowski, Wojciech id: 48C55298-F248-11E8-B48F-1D18A9856A87 last_name: Rzadkowski orcid: 0000-0002-1106-4419 - first_name: N full_name: Defenu, N last_name: Defenu - first_name: S full_name: Chiacchiera, S last_name: Chiacchiera - first_name: A full_name: Trombettoni, A last_name: Trombettoni - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 citation: ama: Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44 apa: Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44 chicago: Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44. ieee: W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020. ista: Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026. mla: Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44. short: W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020). date_created: 2020-10-11T22:01:14Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-07T13:44:16Z day: '01' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/abae44 ec_funded: 1 external_id: isi: - '000573298000001' file: - access_level: open_access checksum: c9238fff422e7a957c3a0d559f756b3a content_type: application/pdf creator: dernst date_created: 2020-10-12T12:18:47Z date_updated: 2020-10-12T12:18:47Z file_id: '8650' file_name: 2020_NewJournalPhysics_Rzdkowski.pdf file_size: 2725143 relation: main_file success: 1 file_date_updated: 2020-10-12T12:18:47Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 05A235A0-7A3F-11EA-A408-12923DDC885E grant_number: '25681' name: Analytic and machine learning approaches to composite quantum impurities - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities publication: New Journal of Physics publication_identifier: issn: - '13672630' publication_status: published publisher: IOP Publishing quality_controlled: '1' related_material: record: - id: '10759' relation: dissertation_contains status: public scopus_import: '1' status: public title: Detecting composite orders in layered models via machine learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2020' ... --- _id: '8705' abstract: - lang: eng text: We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model. acknowledgement: Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria) article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Krzysztof full_name: Mysliwy, Krzysztof id: 316457FC-F248-11E8-B48F-1D18A9856A87 last_name: Mysliwy - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025. doi:10.1007/s00023-020-00969-3 apa: Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-020-00969-3 chicago: Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare. Springer Nature, 2020. https://doi.org/10.1007/s00023-020-00969-3. ieee: K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” Annales Henri Poincare, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020. ista: Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025. mla: Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:10.1007/s00023-020-00969-3. short: K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025. date_created: 2020-10-25T23:01:19Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-07T13:43:51Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00023-020-00969-3 ec_funded: 1 external_id: arxiv: - '2003.12371' isi: - '000578111800002' file: - access_level: open_access checksum: c12c9c1e6f08def245e42f3cb1d83827 content_type: application/pdf creator: cziletti date_created: 2020-10-27T12:49:04Z date_updated: 2020-10-27T12:49:04Z file_id: '8711' file_name: 2020_Annales_Mysliwy.pdf file_size: 469831 relation: main_file success: 1 file_date_updated: 2020-10-27T12:49:04Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4003-4025 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11473' relation: dissertation_contains status: public scopus_import: '1' status: public title: Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '10861' abstract: - lang: eng text: We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance. article_processing_charge: No article_type: original author: - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Olivier full_name: Lebeltel, Olivier last_name: Lebeltel - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dogan full_name: Ulus, Dogan last_name: Ulus citation: ama: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z' apa: 'Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-020-00582-z' chicago: 'Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer. Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.' ieee: 'D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.' ista: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.' mla: 'Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z.' short: D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758. date_created: 2022-03-18T10:10:53Z date_published: 2020-08-03T00:00:00Z date_updated: 2023-09-08T11:52:02Z day: '03' department: - _id: ToHe doi: 10.1007/s10009-020-00582-z external_id: isi: - '000555398600001' intvolume: ' 22' isi: 1 issue: '6' keyword: - Information Systems - Software language: - iso: eng month: '08' oa_version: None page: 741-758 publication: International Journal on Software Tools for Technology Transfer publication_identifier: eissn: - 1433-2787 issn: - 1433-2779 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '299' relation: earlier_version status: public scopus_import: '1' status: public title: 'AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 22 year: '2020' ... --- _id: '14125' abstract: - lang: eng text: "Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively." article_processing_charge: No article_type: original author: - first_name: Stefan G full_name: Stark, Stefan G last_name: Stark - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Rudolf full_name: Aebersold, Rudolf last_name: Aebersold - first_name: Faisal S full_name: Al-Quaddoomi, Faisal S last_name: Al-Quaddoomi - first_name: Jonas full_name: Albinus, Jonas last_name: Albinus - first_name: Ilaria full_name: Alborelli, Ilaria last_name: Alborelli - first_name: Sonali full_name: Andani, Sonali last_name: Andani - first_name: Per-Olof full_name: Attinger, Per-Olof last_name: Attinger - first_name: Marina full_name: Bacac, Marina last_name: Bacac - first_name: Daniel full_name: Baumhoer, Daniel last_name: Baumhoer - first_name: Beatrice full_name: Beck-Schimmer, Beatrice last_name: Beck-Schimmer - first_name: Niko full_name: Beerenwinkel, Niko last_name: Beerenwinkel - first_name: Christian full_name: Beisel, Christian last_name: Beisel - first_name: Lara full_name: Bernasconi, Lara last_name: Bernasconi - first_name: Anne full_name: Bertolini, Anne last_name: Bertolini - first_name: Bernd full_name: Bodenmiller, Bernd last_name: Bodenmiller - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Ruben full_name: Casanova, Ruben last_name: Casanova - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Natalia full_name: Chicherova, Natalia last_name: Chicherova - first_name: Maya full_name: D'Costa, Maya last_name: D'Costa - first_name: Esther full_name: Danenberg, Esther last_name: Danenberg - first_name: Natalie full_name: Davidson, Natalie last_name: Davidson - first_name: Monica-Andreea Dră full_name: gan, Monica-Andreea Dră last_name: gan - first_name: Reinhard full_name: Dummer, Reinhard last_name: Dummer - first_name: Stefanie full_name: Engler, Stefanie last_name: Engler - first_name: Martin full_name: Erkens, Martin last_name: Erkens - first_name: Katja full_name: Eschbach, Katja last_name: Eschbach - first_name: Cinzia full_name: Esposito, Cinzia last_name: Esposito - first_name: André full_name: Fedier, André last_name: Fedier - first_name: Pedro full_name: Ferreira, Pedro last_name: Ferreira - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Anja L full_name: Frei, Anja L last_name: Frei - first_name: Bruno full_name: Frey, Bruno last_name: Frey - first_name: Sandra full_name: Goetze, Sandra last_name: Goetze - first_name: Linda full_name: Grob, Linda last_name: Grob - first_name: Gabriele full_name: Gut, Gabriele last_name: Gut - first_name: Detlef full_name: Günther, Detlef last_name: Günther - first_name: Martina full_name: Haberecker, Martina last_name: Haberecker - first_name: Pirmin full_name: Haeuptle, Pirmin last_name: Haeuptle - first_name: Viola full_name: Heinzelmann-Schwarz, Viola last_name: Heinzelmann-Schwarz - first_name: Sylvia full_name: Herter, Sylvia last_name: Herter - first_name: Rene full_name: Holtackers, Rene last_name: Holtackers - first_name: Tamara full_name: Huesser, Tamara last_name: Huesser - first_name: Anja full_name: Irmisch, Anja last_name: Irmisch - first_name: Francis full_name: Jacob, Francis last_name: Jacob - first_name: Andrea full_name: Jacobs, Andrea last_name: Jacobs - first_name: Tim M full_name: Jaeger, Tim M last_name: Jaeger - first_name: Katharina full_name: Jahn, Katharina last_name: Jahn - first_name: Alva R full_name: James, Alva R last_name: James - first_name: Philip M full_name: Jermann, Philip M last_name: Jermann - first_name: André full_name: Kahles, André last_name: Kahles - first_name: Abdullah full_name: Kahraman, Abdullah last_name: Kahraman - first_name: Viktor H full_name: Koelzer, Viktor H last_name: Koelzer - first_name: Werner full_name: Kuebler, Werner last_name: Kuebler - first_name: Jack full_name: Kuipers, Jack last_name: Kuipers - first_name: Christian P full_name: Kunze, Christian P last_name: Kunze - first_name: Christian full_name: Kurzeder, Christian last_name: Kurzeder - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann - first_name: Mitchell full_name: Levesque, Mitchell last_name: Levesque - first_name: Sebastian full_name: Lugert, Sebastian last_name: Lugert - first_name: Gerd full_name: Maass, Gerd last_name: Maass - first_name: Markus full_name: Manz, Markus last_name: Manz - first_name: Philipp full_name: Markolin, Philipp last_name: Markolin - first_name: Julien full_name: Mena, Julien last_name: Mena - first_name: Ulrike full_name: Menzel, Ulrike last_name: Menzel - first_name: Julian M full_name: Metzler, Julian M last_name: Metzler - first_name: Nicola full_name: Miglino, Nicola last_name: Miglino - first_name: Emanuela S full_name: Milani, Emanuela S last_name: Milani - first_name: Holger full_name: Moch, Holger last_name: Moch - first_name: Simone full_name: Muenst, Simone last_name: Muenst - first_name: Riccardo full_name: Murri, Riccardo last_name: Murri - first_name: Charlotte KY full_name: Ng, Charlotte KY last_name: Ng - first_name: Stefan full_name: Nicolet, Stefan last_name: Nicolet - first_name: Marta full_name: Nowak, Marta last_name: Nowak - first_name: Patrick GA full_name: Pedrioli, Patrick GA last_name: Pedrioli - first_name: Lucas full_name: Pelkmans, Lucas last_name: Pelkmans - first_name: Salvatore full_name: Piscuoglio, Salvatore last_name: Piscuoglio - first_name: Michael full_name: Prummer, Michael last_name: Prummer - first_name: Mathilde full_name: Ritter, Mathilde last_name: Ritter - first_name: Christian full_name: Rommel, Christian last_name: Rommel - first_name: María L full_name: Rosano-González, María L last_name: Rosano-González - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Natascha full_name: Santacroce, Natascha last_name: Santacroce - first_name: Jacobo Sarabia del full_name: Castillo, Jacobo Sarabia del last_name: Castillo - first_name: Ramona full_name: Schlenker, Ramona last_name: Schlenker - first_name: Petra C full_name: Schwalie, Petra C last_name: Schwalie - first_name: Severin full_name: Schwan, Severin last_name: Schwan - first_name: Tobias full_name: Schär, Tobias last_name: Schär - first_name: Gabriela full_name: Senti, Gabriela last_name: Senti - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Sujana full_name: Sivapatham, Sujana last_name: Sivapatham - first_name: Berend full_name: Snijder, Berend last_name: Snijder - first_name: Bettina full_name: Sobottka, Bettina last_name: Sobottka - first_name: Vipin T full_name: Sreedharan, Vipin T last_name: Sreedharan - first_name: Stefan full_name: Stark, Stefan last_name: Stark - first_name: Daniel J full_name: Stekhoven, Daniel J last_name: Stekhoven - first_name: Alexandre PA full_name: Theocharides, Alexandre PA last_name: Theocharides - first_name: Tinu M full_name: Thomas, Tinu M last_name: Thomas - first_name: Markus full_name: Tolnay, Markus last_name: Tolnay - first_name: Vinko full_name: Tosevski, Vinko last_name: Tosevski - first_name: Nora C full_name: Toussaint, Nora C last_name: Toussaint - first_name: Mustafa A full_name: Tuncel, Mustafa A last_name: Tuncel - first_name: Marina full_name: Tusup, Marina last_name: Tusup - first_name: Audrey Van full_name: Drogen, Audrey Van last_name: Drogen - first_name: Marcus full_name: Vetter, Marcus last_name: Vetter - first_name: Tatjana full_name: Vlajnic, Tatjana last_name: Vlajnic - first_name: Sandra full_name: Weber, Sandra last_name: Weber - first_name: Walter P full_name: Weber, Walter P last_name: Weber - first_name: Rebekka full_name: Wegmann, Rebekka last_name: Wegmann - first_name: Michael full_name: Weller, Michael last_name: Weller - first_name: Fabian full_name: Wendt, Fabian last_name: Wendt - first_name: Norbert full_name: Wey, Norbert last_name: Wey - first_name: Andreas full_name: Wicki, Andreas last_name: Wicki - first_name: Bernd full_name: Wollscheid, Bernd last_name: Wollscheid - first_name: Shuqing full_name: Yu, Shuqing last_name: Yu - first_name: Johanna full_name: Ziegler, Johanna last_name: Ziegler - first_name: Marc full_name: Zimmermann, Marc last_name: Zimmermann - first_name: Martin full_name: Zoche, Martin last_name: Zoche - first_name: Gregor full_name: Zuend, Gregor last_name: Zuend - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann citation: ama: 'Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843' apa: 'Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843' chicago: 'Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.' ieee: 'S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.' ista: 'Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.' mla: 'Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.' short: S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927. date_created: 2023-08-21T12:28:20Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-11T10:21:00Z day: '01' department: - _id: FrLo doi: 10.1093/bioinformatics/btaa843 extern: '1' external_id: pmid: - '33381818' intvolume: ' 36' issue: Supplement_2 keyword: - Computational Mathematics - Computational Theory and Mathematics - Computer Science Applications - Molecular Biology - Biochemistry - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/bioinformatics/btaa843 month: '12' oa: 1 oa_version: Published Version page: i919-i927 pmid: 1 publication: Bioinformatics publication_identifier: eissn: - 1367-4811 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ratschlab/scim scopus_import: '1' status: public title: 'SCIM: Universal single-cell matching with unpaired feature sets' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2020' ... --- _id: '14186' abstract: - lang: eng text: "The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research." article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Mario full_name: Lucic, Mario last_name: Lucic - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: 'Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120' apa: 'Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120' chicago: Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120. ieee: F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684. ista: 'Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.' mla: Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120. short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684. conference: end_date: 2020-02-12 location: New York, NY, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2020-02-07 date_created: 2023-08-22T14:07:26Z date_published: 2020-07-28T00:00:00Z date_updated: 2023-09-12T07:44:48Z day: '28' department: - _id: FrLo doi: 10.1609/aaai.v34i09.7120 extern: '1' external_id: arxiv: - '2007.14184' intvolume: ' 34' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.14184 month: '07' oa: 1 oa_version: Preprint page: 13681-13684 publication: The 34th AAAI Conference on Artificial Intelligence publication_identifier: eissn: - 2374-3468 isbn: - '9781577358350' publication_status: published publisher: Association for the Advancement of Artificial Intelligence quality_controlled: '1' scopus_import: '1' status: public title: A commentary on the unsupervised learning of disentangled representations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2020' ... --- _id: '14188' abstract: - lang: eng text: "Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios." alternative_title: - PMLR article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Ben full_name: Poole, Ben last_name: Poole - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen citation: ama: 'Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359.' apa: Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual. chicago: Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020. ieee: F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359. ista: Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359. mla: Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 6348–6359. short: F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359. conference: end_date: 2020-07-18 location: Virtual name: International Conference on Machine Learning start_date: 2020-07-13 date_created: 2023-08-22T14:08:14Z date_published: 2020-07-07T00:00:00Z date_updated: 2023-09-12T07:59:29Z day: '07' department: - _id: FrLo extern: '1' external_id: arxiv: - '2002.02886' intvolume: ' 119' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.02886 month: '07' oa: 1 oa_version: Preprint page: 6348–6359 publication: Proceedings of the 37th International Conference on Machine Learning publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Weakly-supervised disentanglement without compromises type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '14187' abstract: - lang: eng text: "We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package." alternative_title: - PMLR article_processing_charge: No author: - first_name: Geoffrey full_name: Négiar, Geoffrey last_name: Négiar - first_name: Gideon full_name: Dresdner, Gideon last_name: Dresdner - first_name: Alicia full_name: Tsai, Alicia last_name: Tsai - first_name: Laurent El full_name: Ghaoui, Laurent El last_name: Ghaoui - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Robert M. full_name: Freund, Robert M. last_name: Freund - first_name: Fabian full_name: Pedregosa, Fabian last_name: Pedregosa citation: ama: 'Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262.' apa: Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual. chicago: Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020. ieee: G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262. ista: Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262. mla: Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62. short: G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262. conference: end_date: 2020-07-18 location: Virtual name: International Conference on Machine Learning start_date: 2020-07-13 date_created: 2023-08-22T14:07:52Z date_published: 2020-07-27T00:00:00Z date_updated: 2023-09-12T08:03:40Z day: '27' department: - _id: FrLo extern: '1' external_id: arxiv: - '2002.11860' intvolume: ' 119' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.11860 month: '07' oa: 1 oa_version: Preprint page: 7253-7262 publication: Proceedings of the 37th International Conference on Machine Learning publication_status: published quality_controlled: '1' status: public title: Stochastic Frank-Wolfe for constrained finite-sum minimization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '14195' abstract: - lang: eng text: "The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000\r\n models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets." article_number: '209' article_processing_charge: No article_type: original author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Mario full_name: Lucic, Mario last_name: Lucic - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: Locatello F, Bauer S, Lucic M, et al. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 2020;21. apa: Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. MIT Press. chicago: Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research. MIT Press, 2020. ieee: F. Locatello et al., “A sober look at the unsupervised learning of disentangled representations and their evaluation,” Journal of Machine Learning Research, vol. 21. MIT Press, 2020. ista: Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209. mla: Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research, vol. 21, 209, MIT Press, 2020. short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020). date_created: 2023-08-22T14:10:34Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-12T09:23:56Z day: '01' ddc: - '000' department: - _id: FrLo extern: '1' external_id: arxiv: - '2010.14766' has_accepted_license: '1' intvolume: ' 21' language: - iso: eng main_file_link: - open_access: '1' url: https://jmlr.csail.mit.edu/papers/v21/19-976.html month: '09' oa: 1 oa_version: Published Version publication: Journal of Machine Learning Research publication_status: published publisher: MIT Press quality_controlled: '1' scopus_import: '1' status: public title: A sober look at the unsupervised learning of disentangled representations and their evaluation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2020' ... --- _id: '7569' abstract: - lang: eng text: 'Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models.' article_number: e1007642 article_processing_charge: No article_type: original author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642 apa: Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642 chicago: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642. ieee: R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642. mla: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642. short: R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020). date_created: 2020-03-06T07:39:38Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:24Z day: '25' ddc: - '000' - '570' department: - _id: CaGu - _id: GaTk doi: 10.1371/journal.pcbi.1007642 external_id: isi: - '000526725200019' file: - access_level: open_access checksum: 5239dd134dc6e1c71fe7b3ce2953da37 content_type: application/pdf creator: dernst date_created: 2020-03-09T15:12:21Z date_updated: 2020-07-14T12:48:00Z file_id: '7579' file_name: 2020_PlosCompBio_Grah.pdf file_size: 2209325 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: PLOS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9716' relation: research_data status: deleted - id: '9776' relation: research_data status: public - id: '9779' relation: used_in_publication status: public - id: '8155' relation: dissertation_contains status: public - id: '9777' relation: research_data status: public scopus_import: '1' status: public title: The relation between crosstalk and gene regulation form revisited tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2020' ... --- _id: '8813' abstract: - lang: eng text: 'In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.' article_processing_charge: No author: - first_name: Laura full_name: Santini, Laura last_name: Santini - first_name: Florian full_name: Halbritter, Florian last_name: Halbritter - first_name: Fabian full_name: Titz-Teixeira, Fabian last_name: Titz-Teixeira - first_name: Toru full_name: Suzuki, Toru last_name: Suzuki - first_name: Maki full_name: Asami, Maki last_name: Asami - first_name: Julia full_name: Ramesmayer, Julia last_name: Ramesmayer - first_name: Xiaoyan full_name: Ma, Xiaoyan last_name: Ma - first_name: Andreas full_name: Lackner, Andreas last_name: Lackner - first_name: Nick full_name: Warr, Nick last_name: Warr - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Ernest full_name: Laue, Ernest last_name: Laue - first_name: Matthias full_name: Farlik, Matthias last_name: Farlik - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Andreas full_name: Beyer, Andreas last_name: Beyer - first_name: Anthony C. F. full_name: Perry, Anthony C. F. last_name: Perry - first_name: Martin full_name: Leeb, Martin last_name: Leeb citation: ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948 apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948 chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948. ieee: L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory. ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948. mla: Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948. short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.). date_created: 2020-11-26T07:17:19Z date_published: 2020-11-05T00:00:00Z date_updated: 2023-09-12T11:05:28Z day: '05' department: - _id: SiHi doi: 10.1101/2020.11.03.366948 external_id: pmid: - 'PPR234457 ' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.11.03.366948 month: '11' oa: 1 oa_version: Preprint pmid: 1 publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory status: public title: Novel imprints in mouse blastocysts are predominantly DNA methylation independent type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9777' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002 apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002 chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002. ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002. mla: Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:21:51Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:25Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s002 main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pcbi.1007642.s002 month: '02' oa: 1 oa_version: None publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Maximizing crosstalk type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8332' abstract: - lang: eng text: "Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 citation: ama: 'Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332' apa: 'Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332' chicago: 'Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.' ieee: 'B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.' ista: 'Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.' mla: 'Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.' short: 'B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.' date_created: 2020-09-04T12:24:12Z date_published: 2020-09-03T00:00:00Z date_updated: 2023-09-13T08:45:08Z day: '03' ddc: - '000' degree_awarded: PhD department: - _id: ToHe doi: 10.15479/AT:ISTA:8332 file: - access_level: open_access checksum: 26fe261550f691280bda4c454bf015c7 content_type: application/pdf creator: bkragl date_created: 2020-09-04T12:17:47Z date_updated: 2020-09-04T12:17:47Z file_id: '8333' file_name: kragl-thesis.pdf file_size: 1348815 relation: main_file - access_level: closed checksum: b9694ce092b7c55557122adba8337ebc content_type: application/zip creator: bkragl date_created: 2020-09-04T13:00:17Z date_updated: 2020-09-04T13:00:17Z file_id: '8335' file_name: kragl-thesis.zip file_size: 372312 relation: source_file file_date_updated: 2020-09-04T13:00:17Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '120' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '133' relation: part_of_dissertation status: public - id: '8012' relation: part_of_dissertation status: public - id: '8195' relation: part_of_dissertation status: public - id: '160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: 'Verifying concurrent programs: Refinement, synchronization, sequentialization' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '14326' abstract: - lang: eng text: "Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n" article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Dirk full_name: Weissenborn, Dirk last_name: Weissenborn - first_name: Thomas full_name: Unterthiner, Thomas last_name: Unterthiner - first_name: Aravindh full_name: Mahendran, Aravindh last_name: Mahendran - first_name: Georg full_name: Heigold, Georg last_name: Heigold - first_name: Jakob full_name: Uszkoreit, Jakob last_name: Uszkoreit - first_name: Alexey full_name: Dosovitskiy, Alexey last_name: Dosovitskiy - first_name: Thomas full_name: Kipf, Thomas last_name: Kipf citation: ama: 'Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:11525-11538.' apa: 'Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In Advances in Neural Information Processing Systems (Vol. 33, pp. 11525–11538). Virtual: Curran Associates.' chicago: Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In Advances in Neural Information Processing Systems, 33:11525–38. Curran Associates, 2020. ieee: F. Locatello et al., “Object-centric learning with slot attention,” in Advances in Neural Information Processing Systems, Virtual, 2020, vol. 33, pp. 11525–11538. ista: 'Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11525–11538.' mla: Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11525–38. short: F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 11525–11538. conference: end_date: 2020-12-12 location: Virtual name: 'NeurIPS: Neural Information Processing Systems' start_date: 2020-12-06 date_created: 2023-09-13T12:03:46Z date_published: 2020-01-01T00:00:00Z date_updated: 2023-09-13T12:19:19Z department: - _id: FrLo extern: '1' external_id: arxiv: - '2006.15055' intvolume: ' 33' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2006.15055 oa: 1 oa_version: Preprint page: 11525-11538 publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713829546' publication_status: published publisher: Curran Associates quality_controlled: '1' status: public title: Object-centric learning with slot attention type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2020' ... --- _id: '71' abstract: - lang: eng text: "We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric \U0001D54E2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of \U0001D54E2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric." article_processing_charge: No article_type: original author: - first_name: Peter full_name: Gladbach, Peter last_name: Gladbach - first_name: Eva full_name: Kopfer, Eva last_name: Kopfer - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440 apa: Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440 chicago: Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440. ieee: P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020. ista: Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802. mla: Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440. short: P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802. date_created: 2018-12-11T11:44:28Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-09-18T08:13:15Z day: '01' department: - _id: JaMa doi: 10.1137/19M1243440 external_id: arxiv: - '1809.01092' isi: - '000546975100017' intvolume: ' 52' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.01092 month: '10' oa: 1 oa_version: Preprint page: 2759-2802 publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - '10957154' issn: - '00361410' publication_status: published publisher: Society for Industrial and Applied Mathematics publist_id: '7983' quality_controlled: '1' scopus_import: '1' status: public title: Scaling limits of discrete optimal transport type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 52 year: '2020' ... --- _id: '5681' abstract: - lang: eng text: 'We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.' acknowledged_ssus: - _id: ScienComp acknowledgement: This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion. article_processing_charge: No article_type: original author: - first_name: Ibayashi full_name: Hikaru, Ibayashi last_name: Hikaru - 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: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Takeo full_name: Igarashi, Takeo last_name: Igarashi - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando citation: ama: Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628 apa: Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628 chicago: Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628. ieee: I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020. ista: Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302. mla: Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628. short: I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302. date_created: 2018-12-16T22:59:21Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-09-18T09:30:01Z day: '01' ddc: - '006' department: - _id: ChWo doi: 10.1109/TVCG.2018.2883628 external_id: isi: - '000532295600014' pmid: - '30507534' file: - access_level: open_access checksum: 8d4c55443a0ee335bb5bb652de503042 content_type: application/pdf creator: wojtan date_created: 2020-10-08T08:34:53Z date_updated: 2020-10-08T08:34:53Z file_id: '8626' file_name: preprint.pdf file_size: 21910098 relation: main_file success: 1 file_date_updated: 2020-10-08T08:34:53Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 2288-2302 pmid: 1 publication: IEEE Transactions on Visualization and Computer Graphics publication_identifier: eissn: - '19410506' issn: - '10772626' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Simulating liquids on dynamically warping grids type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 26 year: '2020' ... --- _id: '8958' abstract: - lang: eng text: "The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li citation: ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958 apa: Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958 chicago: Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958. ieee: X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020. ista: Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. mla: Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958. short: X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020. date_created: 2020-12-21T09:44:30Z date_published: 2020-12-21T00:00:00Z date_updated: 2023-09-20T11:30:58Z day: '21' ddc: - '539' degree_awarded: PhD department: - _id: MiLe doi: 10.15479/AT:ISTA:8958 ec_funded: 1 file: - access_level: open_access checksum: 3994c54a1241451d561db1d4f43bad30 content_type: application/pdf creator: xli date_created: 2020-12-22T10:55:56Z date_updated: 2020-12-22T10:55:56Z file_id: '8967' file_name: THESIS_Xiang_Li.pdf file_size: 3622305 relation: main_file success: 1 - access_level: closed checksum: 0954ecfc5554c05615c14de803341f00 content_type: application/x-zip-compressed creator: xli date_created: 2020-12-22T10:56:03Z date_updated: 2020-12-30T07:18:03Z file_id: '8968' file_name: THESIS_Xiang_Li.zip file_size: 4018859 relation: source_file file_date_updated: 2020-12-30T07:18:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '125' project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '5886' relation: part_of_dissertation status: public - id: '8587' relation: part_of_dissertation status: public - id: '1120' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Rotation of coupled cold molecules in the presence of a many-body environment type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8386' abstract: - lang: eng text: "Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting." acknowledged_ssus: - _id: SSU acknowledgement: The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X citation: ama: Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386 apa: Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386 chicago: Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386. ieee: R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020. ista: Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. mla: Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386. short: R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020. date_created: 2020-09-14T01:04:53Z date_published: 2020-09-14T00:00:00Z date_updated: 2023-09-22T09:49:31Z day: '14' ddc: - '003' degree_awarded: PhD department: - _id: BeBi doi: 10.15479/AT:ISTA:8386 ec_funded: 1 file: - access_level: closed checksum: edcf578b6e1c9b0dd81ff72d319b66ba content_type: application/x-zip-compressed creator: rzhang date_created: 2020-09-14T01:02:59Z date_updated: 2020-09-14T12:18:43Z file_id: '8388' file_name: Thesis_Ran.zip file_size: 1245800191 relation: source_file - access_level: open_access checksum: 817e20c33be9247f906925517c56a40d content_type: application/pdf creator: rzhang date_created: 2020-09-15T12:51:53Z date_updated: 2020-09-15T12:51:53Z file_id: '8396' file_name: PhD_thesis_Ran Zhang_20200915.pdf file_size: 161385316 relation: main_file success: 1 file_date_updated: 2020-09-15T12:51:53Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '148' project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '486' relation: part_of_dissertation status: public - id: '1002' relation: part_of_dissertation status: public status: public supervisor: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 title: Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7996' abstract: - lang: eng text: "Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka citation: ama: Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996 apa: Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996 chicago: Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996. ieee: J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020. ista: Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. mla: Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996. short: J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020. date_created: 2020-06-22T09:22:23Z date_published: 2020-06-22T00:00:00Z date_updated: 2023-09-26T15:50:22Z day: '22' ddc: - '530' degree_awarded: PhD department: - _id: GeKa doi: 10.15479/AT:ISTA:7996 file: - access_level: closed checksum: 467e52feb3e361ce8cf5fe8d5c254ece content_type: application/x-zip-compressed creator: dernst date_created: 2020-06-22T09:22:04Z date_updated: 2020-07-14T12:48:07Z file_id: '7997' file_name: JK_thesis_latex_source_files.zip file_size: 392794743 relation: main_file - access_level: open_access checksum: 1de716bf110dbd77d383e479232bf496 content_type: application/pdf creator: dernst date_created: 2020-06-22T09:21:29Z date_updated: 2020-07-14T12:48:07Z file_id: '7998' file_name: PhD_thesis_JK_pdfa.pdf file_size: 28453247 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '178' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1328' relation: part_of_dissertation status: public - id: '7541' relation: part_of_dissertation status: public - id: '77' relation: part_of_dissertation status: public - id: '23' relation: part_of_dissertation status: public - id: '840' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8272' abstract: - lang: eng text: We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler citation: ama: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21' apa: Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21 chicago: Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21. ieee: K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420. ista: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.' mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21. short: K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420. conference: name: 'CAV: Computer Aided Verification' date_created: 2020-08-16T22:00:58Z date_published: 2020-07-14T00:00:00Z date_updated: 2023-10-03T11:36:13Z day: '14' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-030-53291-8_21 ec_funded: 1 external_id: arxiv: - '2005.04018' isi: - '000695272500021' file: - access_level: open_access checksum: 093d4788d7d5b2ce0ffe64fbe7820043 content_type: application/pdf creator: dernst date_created: 2020-08-17T11:32:44Z date_updated: 2020-08-17T11:32:44Z file_id: '8276' file_name: 2020_LNCS_CAV_Chatterjee.pdf file_size: 625056 relation: main_file success: 1 file_date_updated: 2020-08-17T11:32:44Z has_accepted_license: '1' intvolume: ' 12225' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 398-420 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: International Conference on Computer Aided Verification publication_identifier: eissn: - '16113349' isbn: - '9783030532901' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '12738' relation: later_version status: public scopus_import: '1' status: public title: Stochastic games with lexicographic reachability-safety objectives 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12225 year: '2020' ... --- _id: '7572' abstract: - lang: eng text: The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material. alternative_title: - Methods in Cell Biology article_processing_charge: No author: - first_name: Paulo R full_name: Dos Santos Caldas, Paulo R id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87 last_name: Dos Santos Caldas orcid: 0000-0001-6730-4461 - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006' apa: Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier. https://doi.org/10.1016/bs.mcb.2020.01.006 chicago: Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61. Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006. ieee: P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161. ista: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.' mla: Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006. short: P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161. date_created: 2020-03-08T23:00:47Z date_published: 2020-02-27T00:00:00Z date_updated: 2023-10-04T09:50:24Z day: '27' department: - _id: MaLo doi: 10.1016/bs.mcb.2020.01.006 ec_funded: 1 editor: - first_name: 'Phong ' full_name: 'Tran, Phong ' last_name: Tran external_id: isi: - '000611826500008' intvolume: ' 158' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/839571 month: '02' oa: 1 oa_version: Preprint page: 145-161 project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: 260D98C8-B435-11E9-9278-68D0E5697425 name: Reconstitution of Bacterial Cell Division Using Purified Components publication: Methods in Cell Biology publication_identifier: issn: - 0091679X publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '8358' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Computational analysis of filament polymerization dynamics in cytoskeletal networks type: book_chapter user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 158 year: '2020' ... --- _id: '7387' abstract: - lang: eng text: Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site. acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V. article_processing_charge: No article_type: letter_note author: - first_name: Natalia S. full_name: Baranova, Natalia S. id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Víctor M. full_name: Hernández-Rocamora, Víctor M. last_name: Hernández-Rocamora - first_name: Carlos full_name: Alfonso, Carlos last_name: Alfonso - first_name: Maria D full_name: Lopez Pelegrin, Maria D id: 319AA9CE-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Pelegrin - first_name: Germán full_name: Rivas, Germán last_name: Rivas - first_name: Waldemar full_name: Vollmer, Waldemar last_name: Vollmer - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5 apa: Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5 chicago: Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5. ieee: N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020. ista: Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417. mla: Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5. short: N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417. date_created: 2020-01-28T16:14:41Z date_published: 2020-01-20T00:00:00Z date_updated: 2023-10-06T12:22:38Z day: '20' department: - _id: MaLo doi: 10.1038/s41564-019-0657-5 ec_funded: 1 external_id: isi: - '000508584700007' pmid: - '31959972' intvolume: ' 5' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://europepmc.org/article/PMC/7048620 month: '01' oa: 1 oa_version: Submitted Version page: 407-417 pmid: 1 project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: 259B655A-B435-11E9-9278-68D0E5697425 grant_number: LT000824/2016 name: Reconstitution of bacterial cell wall sythesis - _id: 2596EAB6-B435-11E9-9278-68D0E5697425 grant_number: ALTF 2015-1163 name: Synthesis of bacterial cell wall publication: Nature Microbiology publication_identifier: issn: - 2058-5276 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/little-cell-big-cover-story/ record: - id: '14280' relation: dissertation_contains status: public scopus_import: '1' status: public title: Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2020' ... --- _id: '8163' abstract: - lang: eng text: Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces. acknowledgement: "The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31." article_processing_charge: No article_type: original author: - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454 apa: Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454 chicago: Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454. ieee: G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020. ista: Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199. mla: Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454. short: G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199. date_created: 2020-07-24T07:09:18Z date_published: 2020-07-24T00:00:00Z date_updated: 2023-10-10T13:05:27Z day: '24' ddc: - '510' department: - _id: HeEd doi: 10.1556/012.2020.57.2.1454 ec_funded: 1 external_id: isi: - '000570978400005' file: - access_level: open_access content_type: application/pdf creator: mwintrae date_created: 2020-07-24T07:09:06Z date_updated: 2020-07-24T07:09:06Z file_id: '8164' file_name: 57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf file_size: 1476072 relation: main_file file_date_updated: 2020-07-24T07:09:06Z has_accepted_license: '1' intvolume: ' 57' isi: 1 issue: '2' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 193-199 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize publication: Studia Scientiarum Mathematicarum Hungarica publication_identifier: eissn: - 1588-2896 issn: - 0081-6906 publication_status: published publisher: Akadémiai Kiadó quality_controlled: '1' scopus_import: '1' status: public title: Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2020' ... --- _id: '8671' abstract: - lang: eng text: 'We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr(''39'')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. ' acknowledgement: We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences. article_processing_charge: No article_type: original author: - first_name: A. full_name: Shakiba, A. last_name: Shakiba - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: M.R. full_name: Hooshmandasl, M.R. last_name: Hooshmandasl - first_name: M. full_name: Alambardar Meybodi, M. last_name: Alambardar Meybodi citation: ama: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117 apa: Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117 chicago: Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117. ieee: A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020. ista: Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128. mla: Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117. short: A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128. date_created: 2020-10-18T22:01:36Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-10-16T09:25:00Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.29252/ijmsi.15.2.117 external_id: arxiv: - '1805.10672' file: - access_level: open_access checksum: f299661a6d51cda6d255a76be696f48d content_type: application/pdf creator: dernst date_created: 2020-10-19T11:14:20Z date_updated: 2020-10-19T11:14:20Z file_id: '8676' file_name: 2020_ijmsi_Shakiba_accepted.pdf file_size: 261688 relation: main_file success: 1 file_date_updated: 2020-10-19T11:14:20Z has_accepted_license: '1' intvolume: ' 15' issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 117-128 project: - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: Iranian Journal of Mathematical Sciences and Informatics publication_identifier: eissn: - 2008-9473 issn: - 1735-4463 publication_status: published publisher: Iranian Academic Center for Education, Culture and Research quality_controlled: '1' scopus_import: '1' status: public title: A note on belief structures and s-approximation spaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2020' ...