--- _id: '12987' abstract: - lang: eng text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome. article_processing_charge: No author: - first_name: Eva full_name: Koch, Eva last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - 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: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4' apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4' chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.' ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.' ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.' mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.' short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021). date_created: 2023-05-16T12:34:09Z date_published: 2021-04-10T00:00:00Z date_updated: 2023-08-08T13:34:07Z day: '10' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.ZGMSBCCB4 has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.zgmsbccb4 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9394' relation: used_in_publication status: public status: public title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis' 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: '2021' ... --- _id: '9408' abstract: - lang: eng text: We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype. acknowledgement: The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767). article_number: 2881-2895 article_processing_charge: No author: - first_name: Xudong full_name: Feng, Xudong last_name: Feng - first_name: Jiafeng full_name: Liu, Jiafeng last_name: Liu - first_name: Huamin full_name: Wang, Huamin last_name: Wang - first_name: Yin full_name: Yang, Yin last_name: Yang - first_name: Hujun full_name: Bao, Hujun last_name: Bao - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Weiwei full_name: Xu, Weiwei last_name: Xu citation: ama: Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218 apa: Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218 chicago: Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218. ieee: X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021. ista: Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895. mla: Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218. short: X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021). date_created: 2021-05-23T22:01:42Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-08T13:45:46Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1109/TVCG.2019.2957218 ec_funded: 1 external_id: isi: - '000649620700009' pmid: - '31804937' file: - access_level: open_access checksum: a78e6ac94e33ade4ffaea66943d5f7dc content_type: application/pdf creator: kschuh date_created: 2021-05-25T15:08:49Z date_updated: 2021-05-25T15:08:49Z file_id: '9427' file_name: 2021_TVCG_Feng.pdf file_size: 6183002 relation: main_file success: 1 file_date_updated: 2021-05-25T15:08:49Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: IEEE Transactions on Visualization and Computer Graphics publication_identifier: eissn: - '10772626' issn: - '19410506' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Computational design of skinned Quad-Robots 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: 27 year: '2021' ... --- _id: '9410' abstract: - lang: eng text: Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains. acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support. article_number: '20200913' article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Paul full_name: Neve, Paul last_name: Neve citation: ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913 apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913 chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913. ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021. ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913. mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913. short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021). date_created: 2021-05-23T22:01:43Z date_published: 2021-05-12T00:00:00Z date_updated: 2023-08-08T13:44:35Z day: '12' ddc: - '570' department: - _id: NiBa doi: 10.1098/rsbl.2020.0913 ec_funded: 1 external_id: isi: - '000651501400001' pmid: - ' 33975485' file: - access_level: open_access checksum: 9c13c1f5af7609c97c741f11d293188a content_type: application/pdf creator: kschuh date_created: 2021-05-25T14:09:03Z date_updated: 2021-05-25T14:09:03Z file_id: '9425' file_name: 2021_BiologyLetters_Lagator.pdf file_size: 726759 relation: main_file success: 1 file_date_updated: 2021-05-25T14:09:03Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology letters publication_identifier: eissn: - 1744957X publication_status: published publisher: Royal Society of London quality_controlled: '1' scopus_import: '1' status: public title: Adaptation at different points along antibiotic concentration gradients 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: 17 year: '2021' ... --- _id: '9412' abstract: - lang: eng text: We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness. article_number: '24' article_processing_charge: No author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP591 apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591 chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” Electronic Journal of Probability, vol. 26. Institute of Mathematical Statistics, 2021. ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24. mla: Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591. short: G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021). date_created: 2021-05-23T22:01:44Z date_published: 2021-03-23T00:00:00Z date_updated: 2023-08-08T13:39:19Z day: '23' ddc: - '510' department: - _id: LaEr doi: 10.1214/21-EJP591 ec_funded: 1 external_id: arxiv: - '2002.02438' isi: - '000641855600001' file: - access_level: open_access checksum: 864ab003ad4cffea783f65aa8c2ba69f content_type: application/pdf creator: kschuh date_created: 2021-05-25T13:24:19Z date_updated: 2021-05-25T13:24:19Z file_id: '9423' file_name: 2021_EJP_Cipolloni.pdf file_size: 865148 relation: main_file success: 1 file_date_updated: 2021-05-25T13:24:19Z has_accepted_license: '1' intvolume: ' 26' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Electronic Journal of Probability publication_identifier: eissn: - '10836489' publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Fluctuation around the circular law for random matrices with real entries 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: 26 year: '2021' ... --- _id: '9407' abstract: - lang: eng text: 'High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios.' acknowledgement: The authors thank Malte Schröder for valuable discussions and creating the scale-free network topologies. B.H. thanks Mukund Vasudevan for helpful discussion. The research by M.T. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy–EXC-2068–390729961–Cluster of Excellence Physics of Life of TU Dresden. article_number: '2586' article_processing_charge: No article_type: original author: - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Marc full_name: Timme, Marc last_name: Timme - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Scarselli D, Budanur NB, Timme M, Hof B. Discontinuous epidemic transition due to limited testing. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-22725-9 apa: Scarselli, D., Budanur, N. B., Timme, M., & Hof, B. (2021). Discontinuous epidemic transition due to limited testing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-22725-9 chicago: Scarselli, Davide, Nazmi B Budanur, Marc Timme, and Björn Hof. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-22725-9. ieee: D. Scarselli, N. B. Budanur, M. Timme, and B. Hof, “Discontinuous epidemic transition due to limited testing,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Scarselli D, Budanur NB, Timme M, Hof B. 2021. Discontinuous epidemic transition due to limited testing. Nature Communications. 12(1), 2586. mla: Scarselli, Davide, et al. “Discontinuous Epidemic Transition Due to Limited Testing.” Nature Communications, vol. 12, no. 1, 2586, Springer Nature, 2021, doi:10.1038/s41467-021-22725-9. short: D. Scarselli, N.B. Budanur, M. Timme, B. Hof, Nature Communications 12 (2021). date_created: 2021-05-23T22:01:42Z date_published: 2021-05-10T00:00:00Z date_updated: 2023-08-08T13:45:13Z day: '10' ddc: - '570' department: - _id: BjHo doi: 10.1038/s41467-021-22725-9 external_id: isi: - '000687305500044' file: - access_level: open_access checksum: fe26c1b8a7da1ae07a6c03f80ff06ea1 content_type: application/pdf creator: kschuh date_created: 2021-05-25T14:18:40Z date_updated: 2021-05-25T14:18:40Z file_id: '9426' file_name: 2021_NatureCommunications_Scarselli.pdf file_size: 1176573 relation: main_file success: 1 file_date_updated: 2021-05-25T14:18:40Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' 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/smashing-the-covid-curve/ scopus_import: '1' status: public title: Discontinuous epidemic transition due to limited testing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9411' abstract: - lang: eng text: The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations. acknowledgement: This work was financially supported by the DFG Priority Programme SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA 4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing time. article_number: '59' article_processing_charge: No author: - first_name: Alexander full_name: Sukhov, Alexander last_name: Sukhov - first_name: Maxime full_name: Hubert, Maxime last_name: Hubert - first_name: Galien M full_name: Grosjean, Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X - first_name: Oleg full_name: Trosman, Oleg last_name: Trosman - first_name: Sebastian full_name: Ziegler, Sebastian last_name: Ziegler - first_name: Ylona full_name: Collard, Ylona last_name: Collard - first_name: Nicolas full_name: Vandewalle, Nicolas last_name: Vandewalle - first_name: Ana Sunčana full_name: Smith, Ana Sunčana last_name: Smith - first_name: Jens full_name: Harting, Jens last_name: Harting citation: ama: Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2 apa: Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2 chicago: Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2. ieee: A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021. ista: Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 44(4), 59. mla: Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2. short: A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard, N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021). date_created: 2021-05-23T22:01:44Z date_published: 2021-04-24T00:00:00Z date_updated: 2023-08-08T13:36:28Z day: '24' ddc: - '530' department: - _id: ScWa doi: 10.1140/epje/s10189-021-00065-2 external_id: isi: - '000643251300001' file: - access_level: open_access checksum: 0ef342d011afbe3c5cb058fda9a3f395 content_type: application/pdf creator: kschuh date_created: 2021-05-25T11:32:14Z date_updated: 2021-05-25T11:32:14Z file_id: '9422' file_name: 2021_EPJE_Sukhov.pdf file_size: 2507870 relation: main_file success: 1 file_date_updated: 2021-05-25T11:32:14Z has_accepted_license: '1' intvolume: ' 44' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: European Physical Journal E publication_identifier: eissn: - 1292895X issn: - '12928941' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Regimes of motion of magnetocapillary swimmers 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: 44 year: '2021' ... --- _id: '9414' abstract: - lang: eng text: Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density. acknowledgement: The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753. article_processing_charge: No article_type: original author: - first_name: Keisuke full_name: Ishihara, Keisuke last_name: Ishihara - first_name: Franziska full_name: Decker, Franziska last_name: Decker - 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: James F. full_name: Pelletier, James F. last_name: Pelletier - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Jan full_name: Brugués, Jan last_name: Brugués - first_name: Timothy J. full_name: Mitchison, Timothy J. last_name: Mitchison citation: ama: Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723 apa: Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723 chicago: Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723. ieee: K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021. ista: Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879. mla: Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723. short: K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879. date_created: 2021-05-23T22:01:45Z date_published: 2021-04-19T00:00:00Z date_updated: 2023-08-08T13:36:02Z day: '19' department: - _id: MaLo doi: 10.1091/MBC.E20-11-0723 ec_funded: 1 external_id: isi: - '000641574700005' intvolume: ' 32' isi: 1 issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/3.0/ main_file_link: - open_access: '1' url: https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723 month: '04' oa: 1 oa_version: Published Version page: 869-879 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: Molecular Biology of the Cell publication_identifier: eissn: - 1939-4586 issn: - 1059-1524 publication_status: published publisher: American Society for Cell Biology quality_controlled: '1' scopus_import: '1' status: public title: Spatial variation of microtubule depolymerization in large asters tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0) short: CC BY-NC-SA (3.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 32 year: '2021' ... --- _id: '9356' abstract: - lang: eng text: 'In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace''s unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision.' acknowledgement: We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). article_number: '9470547' 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. Quantitative and approximate monitoring. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547' apa: 'Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Online: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470547' chicago: Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547. ieee: T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Online, 2021. ista: 'Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547.' mla: Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547. short: T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021. conference: end_date: 2021-07-02 location: Online name: 'LICS: Symposium on Logic in Computer Science' start_date: 2021-06-29 date_created: 2021-04-30T17:30:47Z date_published: 2021-06-29T00:00:00Z date_updated: 2023-08-08T13:52:56Z day: '29' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.1109/LICS52264.2021.9470547 external_id: arxiv: - '2105.08353' isi: - '000947350400021' file: - access_level: open_access checksum: 6e4cba3f72775f479c5b1b75d1a4a0c4 content_type: application/pdf creator: esarac date_created: 2021-06-16T08:23:54Z date_updated: 2021-06-16T08:23:54Z file_id: '9557' file_name: qam.pdf file_size: 641990 relation: main_file success: 1 file_date_updated: 2021-06-16T08:23:54Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Quantitative and approximate monitoring type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9439' abstract: - lang: eng text: The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks. acknowledgement: We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute. article_processing_charge: No article_type: original author: - first_name: Wiktor F full_name: Mlynarski, Wiktor F id: 358A453A-F248-11E8-B48F-1D18A9856A87 last_name: Mlynarski - first_name: Ann M. full_name: Hermundstad, Ann M. last_name: Hermundstad citation: ama: Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0 apa: Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0 chicago: Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0. ieee: W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021. ista: Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009. mla: Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0. short: W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009. date_created: 2021-05-30T22:01:24Z date_published: 2021-05-20T00:00:00Z date_updated: 2023-08-08T13:51:14Z day: '20' department: - _id: GaTk doi: 10.1038/s41593-021-00846-0 ec_funded: 1 external_id: isi: - '000652577300003' intvolume: ' 24' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/669200 ' month: '05' oa: 1 oa_version: Preprint page: 998-1009 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Neuroscience publication_identifier: eissn: - 1546-1726 issn: - 1097-6256 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Efficient and adaptive sensory codes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 24 year: '2021' ... --- _id: '9443' abstract: - lang: eng text: Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress. acknowledgement: "We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding" article_processing_charge: No article_type: original author: - first_name: N full_name: Ruiz-Lopez, N last_name: Ruiz-Lopez - first_name: J full_name: Pérez-Sancho, J last_name: Pérez-Sancho - first_name: A full_name: Esteban Del Valle, A last_name: Esteban Del Valle - first_name: RP full_name: Haslam, RP last_name: Haslam - first_name: S full_name: Vanneste, S last_name: Vanneste - first_name: R full_name: Catalá, R last_name: Catalá - first_name: C full_name: Perea-Resa, C last_name: Perea-Resa - first_name: D full_name: Van Damme, D last_name: Van Damme - first_name: S full_name: García-Hernández, S last_name: García-Hernández - first_name: A full_name: Albert, A last_name: Albert - first_name: J full_name: Vallarino, J last_name: Vallarino - first_name: J full_name: Lin, J last_name: Lin - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: AP full_name: Macho, AP last_name: Macho - first_name: J full_name: Salinas, J last_name: Salinas - first_name: A full_name: Rosado, A last_name: Rosado - first_name: JA full_name: Napier, JA last_name: Napier - first_name: V full_name: Amorim-Silva, V last_name: Amorim-Silva - first_name: MA full_name: Botella, MA last_name: Botella citation: ama: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122 apa: Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122 chicago: Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122. ieee: N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021. ista: Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453. mla: Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122. short: N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453. date_created: 2021-06-02T13:13:58Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-08-08T13:54:32Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/plcell/koab122 ec_funded: 1 external_id: isi: - '000703938100026' pmid: - '33944955' file: - access_level: open_access checksum: 22d596678d00310d793611864a6d0fcd content_type: application/pdf creator: cchlebak date_created: 2021-10-14T13:36:38Z date_updated: 2021-10-14T13:36:38Z file_id: '10141' file_name: 2021_PlantCell_RuizLopez.pdf file_size: 2952028 relation: main_file success: 1 file_date_updated: 2021-10-14T13:36:38Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '7' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: 2431-2453 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 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: Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress 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: 33 year: '2021' ... --- _id: '9431' abstract: - lang: eng text: Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: EM-Fac acknowledgement: This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). article_number: '3226' article_processing_charge: No article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr - first_name: Clifton L. full_name: Ricana, Clifton L. last_name: Ricana - first_name: Nadia full_name: Nikulin, Nadia last_name: Nikulin - first_name: Jon-Philip R. full_name: Feathers, Jon-Philip R. last_name: Feathers - first_name: Marco full_name: Klanschnig, Marco last_name: Klanschnig - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Marc C. full_name: Johnson, Marc C. last_name: Johnson - first_name: Volker M. full_name: Vogt, Volker M. last_name: Vogt - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick citation: ama: Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0 apa: Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0 chicago: Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0. ieee: M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021. ista: Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226. mla: Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0. short: M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021). date_created: 2021-05-28T14:25:50Z date_published: 2021-05-28T00:00:00Z date_updated: 2023-08-08T13:53:53Z day: '28' ddc: - '570' department: - _id: FlSc doi: 10.1038/s41467-021-23506-0 external_id: isi: - '000659145000011' file: - access_level: open_access checksum: 53ccc53d09a9111143839dbe7784e663 content_type: application/pdf creator: kschuh date_created: 2021-06-09T15:21:14Z date_updated: 2021-06-09T15:21:14Z file_id: '9538' file_name: 2021_NatureCommunications_Obr.pdf file_size: 6166295 relation: main_file success: 1 file_date_updated: 2021-06-09T15:21:14Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Nature Research quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-retroviruses-become-infectious/ scopus_import: '1' status: public title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9467' abstract: - lang: eng text: "Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter \U0001D436, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for \U0001D436≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical \U0001D436=\U0001D436\U0001D450\U0001D45F(\U0001D445\U0001D452) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation." acknowledgement: The anonymous referees are kindly acknowledged for their useful suggestions andcomments. article_number: A17 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Elena full_name: Marensi, Elena id: 0BE7553A-1004-11EA-B805-18983DDC885E last_name: Marensi - first_name: Shuisheng full_name: He, Shuisheng last_name: He - first_name: Ashley P. full_name: Willis, Ashley P. last_name: Willis citation: ama: Marensi E, He S, Willis AP. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 2021;919. doi:10.1017/jfm.2021.371 apa: Marensi, E., He, S., & Willis, A. P. (2021). Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2021.371 chicago: Marensi, Elena, Shuisheng He, and Ashley P. Willis. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2021. https://doi.org/10.1017/jfm.2021.371. ieee: E. Marensi, S. He, and A. P. Willis, “Suppression of turbulence and travelling waves in a vertical heated pipe,” Journal of Fluid Mechanics, vol. 919. Cambridge University Press, 2021. ista: Marensi E, He S, Willis AP. 2021. Suppression of turbulence and travelling waves in a vertical heated pipe. Journal of Fluid Mechanics. 919, A17. mla: Marensi, Elena, et al. “Suppression of Turbulence and Travelling Waves in a Vertical Heated Pipe.” Journal of Fluid Mechanics, vol. 919, A17, Cambridge University Press, 2021, doi:10.1017/jfm.2021.371. short: E. Marensi, S. He, A.P. Willis, Journal of Fluid Mechanics 919 (2021). date_created: 2021-06-06T22:01:30Z date_published: 2021-07-25T00:00:00Z date_updated: 2023-08-08T13:58:41Z day: '25' ddc: - '530' department: - _id: BjHo doi: 10.1017/jfm.2021.371 external_id: arxiv: - '2008.13486' isi: - '000653785000001' file: - access_level: open_access checksum: 867ad077e45c181c2c5ec1311ba27c41 content_type: application/pdf creator: kschuh date_created: 2021-08-03T09:53:28Z date_updated: 2021-08-03T09:53:28Z file_id: '9766' file_name: 2021_JournalFluidMechanics_Marensi.pdf file_size: 4087358 relation: main_file success: 1 file_date_updated: 2021-08-03T09:53:28Z has_accepted_license: '1' intvolume: ' 919' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Journal of Fluid Mechanics publication_identifier: eissn: - '14697645' issn: - '00221120' publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Suppression of turbulence and travelling waves in a vertical heated pipe 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: 919 year: '2021' ... --- _id: '9470' abstract: - lang: eng text: A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance. acknowledgement: We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018). article_processing_charge: No author: - first_name: Emma L. full_name: Berdan, Emma L. last_name: Berdan - first_name: Alexandre full_name: Blanckaert, Alexandre last_name: Blanckaert - first_name: Tanja full_name: Slotte, Tanja last_name: Slotte - first_name: Alexander full_name: Suh, Alexander last_name: Suh - 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: Inês full_name: Fragata, Inês last_name: Fragata citation: ama: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936' apa: 'Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936' chicago: 'Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.' ieee: 'E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.' ista: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.' mla: 'Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.' short: E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723. date_created: 2021-06-06T22:01:31Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-08T13:59:18Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.15936 ec_funded: 1 external_id: isi: - '000652056400001' file: - access_level: open_access checksum: e6f4731365bde2614b333040a08265d8 content_type: application/pdf creator: kschuh date_created: 2021-06-11T15:34:53Z date_updated: 2021-06-11T15:34:53Z file_id: '9545' file_name: 2021_MolecularEcology_Berdan.pdf file_size: 1031978 relation: main_file success: 1 file_date_updated: 2021-06-11T15:34:53Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '06' oa: 1 oa_version: Published Version page: 2710-2723 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Molecular Ecology publication_identifier: eissn: - 1365294X issn: - '09621083' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Unboxing mutations: Connecting mutation types with evolutionary consequences' 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 30 year: '2021' ... --- _id: '9468' abstract: - lang: eng text: "Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\\gamma_e$ such that the only vertices in $\\gamma_e$ are the ends of $e$; (2) if $e\\ne f$, then $\\gamma_e\\cap\\gamma_f$ has precisely two crossings; and (3) if $e\\ne f$, then $e$ intersects $\\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.\r\n" article_processing_charge: No article_type: original 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: R. Bruce full_name: Richter, R. Bruce last_name: Richter - first_name: Matthew full_name: Sunohara, Matthew last_name: Sunohara citation: ama: Arroyo Guevara AM, Richter RB, Sunohara M. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 2021;35(2):1050-1076. doi:10.1137/20M1313234 apa: Arroyo Guevara, A. M., Richter, R. B., & Sunohara, M. (2021). Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1313234 chicago: Arroyo Guevara, Alan M, R. Bruce Richter, and Matthew Sunohara. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2021. https://doi.org/10.1137/20M1313234. ieee: A. M. Arroyo Guevara, R. B. Richter, and M. Sunohara, “Extending drawings of complete graphs into arrangements of pseudocircles,” SIAM Journal on Discrete Mathematics, vol. 35, no. 2. Society for Industrial and Applied Mathematics, pp. 1050–1076, 2021. ista: Arroyo Guevara AM, Richter RB, Sunohara M. 2021. Extending drawings of complete graphs into arrangements of pseudocircles. SIAM Journal on Discrete Mathematics. 35(2), 1050–1076. mla: Arroyo Guevara, Alan M., et al. “Extending Drawings of Complete Graphs into Arrangements of Pseudocircles.” SIAM Journal on Discrete Mathematics, vol. 35, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 1050–76, doi:10.1137/20M1313234. short: A.M. Arroyo Guevara, R.B. Richter, M. Sunohara, SIAM Journal on Discrete Mathematics 35 (2021) 1050–1076. date_created: 2021-06-06T22:01:30Z date_published: 2021-05-20T00:00:00Z date_updated: 2023-08-08T13:58:12Z day: '20' department: - _id: UlWa doi: 10.1137/20M1313234 ec_funded: 1 external_id: arxiv: - '2001.06053' isi: - '000674142200022' intvolume: ' 35' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2001.06053 month: '05' oa: 1 oa_version: Preprint page: 1050-1076 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: SIAM Journal on Discrete Mathematics publication_identifier: issn: - '08954801' publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Extending drawings of complete graphs into arrangements of pseudocircles type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 35 year: '2021' ... --- _id: '9462' abstract: - lang: eng text: We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions. acknowledgement: Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851. article_number: '109096' article_processing_charge: No article_type: original author: - first_name: Andreas full_name: Deuchert, Andreas last_name: Deuchert - 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. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096 apa: Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096 chicago: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096. ieee: A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021. ista: Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096. mla: Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096. short: A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021). date_created: 2021-06-06T22:01:28Z date_published: 2021-09-15T00:00:00Z date_updated: 2023-08-08T13:56:27Z day: '15' department: - _id: RoSe doi: 10.1016/j.jfa.2021.109096 ec_funded: 1 external_id: arxiv: - '2009.00992' isi: - '000656508600008' intvolume: ' 281' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2009.00992 month: '09' oa: 1 oa_version: Preprint project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Journal of Functional Analysis publication_identifier: eissn: - 1096-0783 issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 281 year: '2021' ... --- _id: '9469' abstract: - lang: eng text: In this paper, we consider reflected three-operator splitting methods for monotone inclusion problems in real Hilbert spaces. To do this, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping in real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. We then apply our results to three-operator splitting for the monotone inclusion problem and consequently obtain the corresponding convergence analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured monotone inclusion problems. Some numerical implementations are drawn from splitting methods to support the theoretical analysis. acknowledgement: The authors are grateful to the anonymous referees and the handling Editor for their insightful comments which have improved the earlier version of the manuscript greatly. The second author is grateful to the University of Hafr Al Batin. The last author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160). article_processing_charge: No article_type: original author: - first_name: Olaniyi S. full_name: Iyiola, Olaniyi S. last_name: Iyiola - first_name: Cyril D. full_name: Enyi, Cyril D. last_name: Enyi - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 citation: ama: Iyiola OS, Enyi CD, Shehu Y. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. 2021. doi:10.1080/10556788.2021.1924715 apa: Iyiola, O. S., Enyi, C. D., & Shehu, Y. (2021). Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. Taylor and Francis. https://doi.org/10.1080/10556788.2021.1924715 chicago: Iyiola, Olaniyi S., Cyril D. Enyi, and Yekini Shehu. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software. Taylor and Francis, 2021. https://doi.org/10.1080/10556788.2021.1924715. ieee: O. S. Iyiola, C. D. Enyi, and Y. Shehu, “Reflected three-operator splitting method for monotone inclusion problem,” Optimization Methods and Software. Taylor and Francis, 2021. ista: Iyiola OS, Enyi CD, Shehu Y. 2021. Reflected three-operator splitting method for monotone inclusion problem. Optimization Methods and Software. mla: Iyiola, Olaniyi S., et al. “Reflected Three-Operator Splitting Method for Monotone Inclusion Problem.” Optimization Methods and Software, Taylor and Francis, 2021, doi:10.1080/10556788.2021.1924715. short: O.S. Iyiola, C.D. Enyi, Y. Shehu, Optimization Methods and Software (2021). date_created: 2021-06-06T22:01:30Z date_published: 2021-05-12T00:00:00Z date_updated: 2023-08-08T13:57:43Z day: '12' department: - _id: VlKo doi: 10.1080/10556788.2021.1924715 ec_funded: 1 external_id: isi: - '000650507600001' isi: 1 language: - iso: eng month: '05' oa_version: None project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Optimization Methods and Software publication_identifier: eissn: - 1029-4937 issn: - 1055-6788 publication_status: published publisher: Taylor and Francis quality_controlled: '1' scopus_import: '1' status: public title: Reflected three-operator splitting method for monotone inclusion problem type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9540' abstract: - lang: eng text: The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases. acknowledged_ssus: - _id: EM-Fac acknowledgement: We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.). article_number: '3483' article_processing_charge: No article_type: original author: - first_name: Michael full_name: Prattes, Michael last_name: Prattes - first_name: Irina full_name: Grishkovskaya, Irina last_name: Grishkovskaya - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Ingrid full_name: Rössler, Ingrid last_name: Rössler - first_name: Isabella full_name: Klein, Isabella last_name: Klein - first_name: Christina full_name: Hetzmannseder, Christina last_name: Hetzmannseder - first_name: Gertrude full_name: Zisser, Gertrude last_name: Zisser - first_name: Christian C. full_name: Gruber, Christian C. last_name: Gruber - first_name: Karl full_name: Gruber, Karl last_name: Gruber - first_name: David full_name: Haselbach, David last_name: Haselbach - first_name: Helmut full_name: Bergler, Helmut last_name: Bergler citation: ama: Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x apa: Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x chicago: Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x. ieee: M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483. mla: Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x. short: M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021). date_created: 2021-06-10T14:57:45Z date_published: 2021-06-09T00:00:00Z date_updated: 2023-08-08T14:05:26Z day: '09' ddc: - '570' department: - _id: EM-Fac doi: 10.1038/s41467-021-23854-x external_id: isi: - '000664874700014' pmid: - '34108481' file: - access_level: open_access checksum: 40fc24c1310930990b52a8ad1142ee97 content_type: application/pdf creator: cziletti date_created: 2021-06-15T18:55:59Z date_updated: 2021-06-15T18:55:59Z file_id: '9556' file_name: 2021_NatureComm_Prattes.pdf file_size: 3397292 relation: main_file success: 1 file_date_updated: 2021-06-15T18:55:59Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9549' abstract: - lang: eng text: 'AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. ' acknowledgement: We thank members of the Greger laboratory, B. Herguedas, J. Krieger and J.-N. Dohrke for comments on the manuscript; J. Krieger and J.-N. Dohrke for discussion, J. Krieger for help with the normal mode analysis, B. Köhegyi for help with cryo-EM imaging, V. Chang and K. Suzuki for helping to generate the CNIH2-1D4-HA stable cell line, M. Carvalho for assistance at early stages of this project, the LMB scientific computing and the cryo-EM facility for support, P. Emsley for help with model building, T. Nakane for helpful comments with RELION 3.1 and R. Warshamanage for helping with EMDA cryo-EM-map processing. We acknowledge the Diamond Light Source for access and support of the Cryo-EM facilities at the UK national electron bio10 imaging centre (eBIC), proposal EM17434, funded by the Wellcome Trust, MRC and BBSRC. This work was supported by grants from the Medical Research Council, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation) (MC_U105174197) and BBSRC (BB/N002113/1) to I.H.G. article_processing_charge: No article_type: original author: - first_name: Danyang full_name: Zhang, Danyang last_name: Zhang - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Peter M. full_name: Matthews, Peter M. last_name: Matthews - first_name: Ondrej full_name: Cais, Ondrej last_name: Cais - first_name: Ingo H. full_name: Greger, Ingo H. last_name: Greger citation: ama: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 2021;594:454-458. doi:10.1038/s41586-021-03613-0 apa: Zhang, D., Watson, J., Matthews, P. M., Cais, O., & Greger, I. H. (2021). Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03613-0 chicago: Zhang, Danyang, Jake Watson, Peter M. Matthews, Ondrej Cais, and Ingo H. Greger. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03613-0. ieee: D. Zhang, J. Watson, P. M. Matthews, O. Cais, and I. H. Greger, “Gating and modulation of a hetero-octameric AMPA glutamate receptor,” Nature, vol. 594. Springer Nature, pp. 454–458, 2021. ista: Zhang D, Watson J, Matthews PM, Cais O, Greger IH. 2021. Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature. 594, 454–458. mla: Zhang, Danyang, et al. “Gating and Modulation of a Hetero-Octameric AMPA Glutamate Receptor.” Nature, vol. 594, Springer Nature, 2021, pp. 454–58, doi:10.1038/s41586-021-03613-0. short: D. Zhang, J. Watson, P.M. Matthews, O. Cais, I.H. Greger, Nature 594 (2021) 454–458. date_created: 2021-06-13T22:01:33Z date_published: 2021-06-02T00:00:00Z date_updated: 2023-08-08T13:59:51Z day: '02' department: - _id: PeJo doi: 10.1038/s41586-021-03613-0 external_id: isi: - '000657238100003' pmid: - '34079129' intvolume: ' 594' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41586-021-03613-0 month: '06' oa: 1 oa_version: Published Version page: 454-458 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Gating and modulation of a hetero-octameric AMPA glutamate receptor type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 594 year: '2021' ... --- _id: '9550' abstract: - lang: eng text: 'We prove that the energy of any eigenvector of a sum of several independent large Wigner matrices is equally distributed among these matrices with very high precision. This shows a particularly strong microcanonical form of the equipartition principle for quantum systems whose components are modelled by Wigner matrices. ' acknowledgement: The first author is supported in part by Hong Kong RGC Grant GRF 16301519 and NSFC 11871425. The second author is supported in part by ERC Advanced Grant RANMAT 338804. The third author is supported in part by Swedish Research Council Grant VR-2017-05195 and the Knut and Alice Wallenberg Foundation article_number: e44 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 id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Bao Z, Erdös L, Schnelli K. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2021;9. doi:10.1017/fms.2021.38 apa: Bao, Z., Erdös, L., & Schnelli, K. (2021). Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2021.38 chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2021. https://doi.org/10.1017/fms.2021.38. ieee: Z. Bao, L. Erdös, and K. Schnelli, “Equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 9. Cambridge University Press, 2021. ista: Bao Z, Erdös L, Schnelli K. 2021. Equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 9, e44. mla: Bao, Zhigang, et al. “Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 9, e44, Cambridge University Press, 2021, doi:10.1017/fms.2021.38. short: Z. Bao, L. Erdös, K. Schnelli, Forum of Mathematics, Sigma 9 (2021). date_created: 2021-06-13T22:01:33Z date_published: 2021-05-27T00:00:00Z date_updated: 2023-08-08T14:03:40Z day: '27' ddc: - '510' department: - _id: LaEr doi: 10.1017/fms.2021.38 ec_funded: 1 external_id: arxiv: - '2008.07061' isi: - '000654960800001' file: - access_level: open_access checksum: 47c986578de132200d41e6d391905519 content_type: application/pdf creator: cziletti date_created: 2021-06-15T14:40:45Z date_updated: 2021-06-15T14:40:45Z file_id: '9555' file_name: 2021_ForumMath_Bao.pdf file_size: 483458 relation: main_file success: 1 file_date_updated: 2021-06-15T14:40:45Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Forum of Mathematics, Sigma publication_identifier: eissn: - '20505094' publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Equipartition principle for Wigner matrices 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: '2021' ... --- _id: '9570' abstract: - lang: eng text: We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity. acknowledgement: We acknowledge insightful discussions with K. Flensberg, E. B. Hansen, T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work. article_number: '235201' article_processing_charge: No article_type: original author: - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia - first_name: E. A. full_name: Martinez, E. A. last_name: Martinez - first_name: G. C. full_name: Ménard, G. C. last_name: Ménard - first_name: A. full_name: Pöschl, A. last_name: Pöschl - first_name: S. full_name: Gronin, S. last_name: Gronin - first_name: G. C. full_name: Gardner, G. C. last_name: Gardner - first_name: R. full_name: Kallaher, R. last_name: Kallaher - first_name: M. J. full_name: Manfra, M. J. last_name: Manfra - first_name: C. M. full_name: Marcus, C. M. last_name: Marcus - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: L. full_name: Casparis, L. last_name: Casparis citation: ama: Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 2021;103(23). doi:10.1103/PhysRevB.103.235201 apa: Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner, G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.103.235201 chicago: Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G. C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/PhysRevB.103.235201. ieee: D. Puglia et al., “Closing of the induced gap in a hybrid superconductor-semiconductor nanowire,” Physical Review B, vol. 103, no. 23. American Physical Society, 2021. ista: Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23), 235201. mla: Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Physical Review B, vol. 103, no. 23, 235201, American Physical Society, 2021, doi:10.1103/PhysRevB.103.235201. short: D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner, R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical Review B 103 (2021). date_created: 2021-06-20T22:01:33Z date_published: 2021-06-15T00:00:00Z date_updated: 2023-08-08T14:08:08Z day: '15' department: - _id: AnHi doi: 10.1103/PhysRevB.103.235201 external_id: arxiv: - '2006.01275' isi: - '000661512500002' intvolume: ' 103' isi: 1 issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2006.01275 month: '06' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - '24699969' issn: - '24699950' publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '13080' relation: research_data status: public scopus_import: '1' status: public title: Closing of the induced gap in a hybrid superconductor-semiconductor nanowire type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 103 year: '2021' ...