[{"acknowledgement":"We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship (ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738 to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B.","oa":1,"quality_controlled":"1","publisher":"Embo Press","year":"2020","isi":1,"has_accepted_license":"1","publication":"The Embo Journal","day":"01","date_created":"2020-07-21T09:08:38Z","date_published":"2020-09-01T00:00:00Z","doi":"10.15252/embj.2019104238","article_number":"e104238","project":[{"grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ieee":"J. C. Montesinos López et al., “Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage,” The Embo Journal, vol. 39, no. 17. Embo Press, 2020.","short":"J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös, J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020).","ama":"Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 2020;39(17). doi:10.15252/embj.2019104238","apa":"Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös, K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. Embo Press. https://doi.org/10.15252/embj.2019104238","mla":"Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal, vol. 39, no. 17, e104238, Embo Press, 2020, doi:10.15252/embj.2019104238.","ista":"Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 39(17), e104238.","chicago":"Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia, Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” The Embo Journal. Embo Press, 2020. https://doi.org/10.15252/embj.2019104238."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000548311800001"],"pmid":["32667089"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C"},{"first_name":"A","full_name":"Abuzeineh, A","last_name":"Abuzeineh"},{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"first_name":"Alba","id":"40F05888-F248-11E8-B48F-1D18A9856A87","last_name":"Juanes Garcia","full_name":"Juanes Garcia, Alba","orcid":"0000-0002-1009-9652"},{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Petrášek","full_name":"Petrášek, J","first_name":"J"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"title":"Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 39","month":"09","publication_status":"published","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-12-02T09:13:23Z","file_name":"2020_EMBO_Montesinos.pdf","date_updated":"2020-12-02T09:13:23Z","file_size":3497156,"creator":"dernst","file_id":"8827","checksum":"43d2b36598708e6ab05c69074e191d57","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"issue":"17","volume":39,"_id":"8142","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-05T13:05:47Z","ddc":["580"],"department":[{"_id":"MiSi"},{"_id":"EvBe"}],"file_date_updated":"2020-12-02T09:13:23Z"},{"intvolume":" 40","month":"01","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.","lang":"eng"}],"ec_funded":1,"volume":40,"issue":"1","language":[{"iso":"eng"}],"file":[{"file_id":"8150","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-07-22T11:44:48Z","file_name":"2020_JournNeuroscience_Lombardi.pdf","creator":"dernst","date_updated":"2020-07-22T11:44:48Z","file_size":6646046}],"publication_status":"published","publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"status":"public","type":"journal_article","article_type":"original","_id":"8084","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-22T11:44:48Z","ddc":["570"],"date_updated":"2023-09-05T14:02:55Z","oa":1,"publisher":"Society for Neuroscience","quality_controlled":"1","date_created":"2020-07-05T15:24:51Z","date_published":"2020-01-02T00:00:00Z","doi":"10.1523/jneurosci.1278-19.2019","page":"171-190","publication":"Journal of Neuroscience","day":"02","year":"2020","isi":1,"has_accepted_license":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"title":"Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake","external_id":{"pmid":["31694962"],"isi":["000505167600016"]},"article_processing_charge":"No","author":[{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"full_name":"Gómez-Extremera, Manuel","last_name":"Gómez-Extremera","first_name":"Manuel"},{"full_name":"Bernaola-Galván, Pedro","last_name":"Bernaola-Galván","first_name":"Pedro"},{"first_name":"Ramalingam","last_name":"Vetrivelan","full_name":"Vetrivelan, Ramalingam"},{"first_name":"Clifford B.","last_name":"Saper","full_name":"Saper, Clifford B."},{"first_name":"Thomas E.","last_name":"Scammell","full_name":"Scammell, Thomas E."},{"first_name":"Plamen Ch.","full_name":"Ivanov, Plamen Ch.","last_name":"Ivanov"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Lombardi F, Gómez-Extremera M, Bernaola-Galván P, Vetrivelan R, Saper CB, Scammell TE, Ivanov PC. 2020. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 40(1), 171–190.","chicago":"Lombardi, Fabrizio, Manuel Gómez-Extremera, Pedro Bernaola-Galván, Ramalingam Vetrivelan, Clifford B. Saper, Thomas E. Scammell, and Plamen Ch. Ivanov. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/jneurosci.1278-19.2019.","ama":"Lombardi F, Gómez-Extremera M, Bernaola-Galván P, et al. Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. 2020;40(1):171-190. doi:10.1523/jneurosci.1278-19.2019","apa":"Lombardi, F., Gómez-Extremera, M., Bernaola-Galván, P., Vetrivelan, R., Saper, C. B., Scammell, T. E., & Ivanov, P. C. (2020). Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.1278-19.2019","ieee":"F. Lombardi et al., “Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake,” Journal of Neuroscience, vol. 40, no. 1. Society for Neuroscience, pp. 171–190, 2020.","short":"F. Lombardi, M. Gómez-Extremera, P. Bernaola-Galván, R. Vetrivelan, C.B. Saper, T.E. Scammell, P.C. Ivanov, Journal of Neuroscience 40 (2020) 171–190.","mla":"Lombardi, Fabrizio, et al. “Critical Dynamics and Coupling in Bursts of Cortical Rhythms Indicate Non-Homeostatic Mechanism for Sleep-Stage Transitions and Dual Role of VLPO Neurons in Both Sleep and Wake.” Journal of Neuroscience, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 171–90, doi:10.1523/jneurosci.1278-19.2019."}},{"_id":"7650","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2023-09-05T14:18:49Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-11-20T13:17:42Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider a dilute, homogeneous Bose gas at positive temperature. The system is investigated in the Gross–Pitaevskii limit, where the scattering length a is so small that the interaction energy is of the same order of magnitude as the spectral gap of the Laplacian, and for temperatures that are comparable to the critical temperature of the ideal gas. We show that the difference between the specific free energy of the interacting system and the one of the ideal gas is to leading order given by 4πa(2ϱ2−ϱ20). Here ϱ denotes the density of the system and ϱ0 is the expected condensate density of the ideal gas. Additionally, we show that the one-particle density matrix of any approximate minimizer of the Gibbs free energy functional is to leading order given by the one of the ideal gas. This in particular proves Bose–Einstein condensation with critical temperature given by the one of the ideal gas to leading order. One key ingredient of our proof is a novel use of the Gibbs variational principle that goes hand in hand with the c-number substitution."}],"month":"03","intvolume":" 236","scopus_import":"1","file":[{"success":1,"file_id":"8785","checksum":"b645fb64bfe95bbc05b3eea374109a9c","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_ArchRatMechanicsAnalysis_Deuchert.pdf","date_created":"2020-11-20T13:17:42Z","file_size":704633,"date_updated":"2020-11-20T13:17:42Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"publication_status":"published","issue":"6","volume":236,"ec_funded":1,"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Deuchert and R. Seiringer, “Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature,” Archive for Rational Mechanics and Analysis, vol. 236, no. 6. Springer Nature, pp. 1217–1271, 2020.","short":"A. Deuchert, R. Seiringer, Archive for Rational Mechanics and Analysis 236 (2020) 1217–1271.","apa":"Deuchert, A., & Seiringer, R. (2020). Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01489-4","ama":"Deuchert A, Seiringer R. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 2020;236(6):1217-1271. doi:10.1007/s00205-020-01489-4","mla":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis, vol. 236, no. 6, Springer Nature, 2020, pp. 1217–71, doi:10.1007/s00205-020-01489-4.","ista":"Deuchert A, Seiringer R. 2020. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 236(6), 1217–1271.","chicago":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01489-4."},"title":"Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature","author":[{"last_name":"Deuchert","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000519415000001"],"arxiv":["1901.11363"]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). It is a pleasure to thank Jakob Yngvason for helpful discussions. Financial support by the European Research Council (ERC) under the European Union’sHorizon 2020 research and innovation programme (Grant Agreement No. 694227) is gratefully acknowledged. A. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 836146.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"09","publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-03-09T00:00:00Z","doi":"10.1007/s00205-020-01489-4","date_created":"2020-04-08T15:18:03Z","page":"1217-1271"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential."}],"intvolume":" 238","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2020-12-02T08:50:38Z","file_name":"2020_ArchiveRatMech_Bossmann.pdf","creator":"dernst","date_updated":"2020-12-02T08:50:38Z","file_size":942343,"checksum":"cc67a79a67bef441625fcb1cd031db3d","file_id":"8826","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"ec_funded":1,"volume":238,"issue":"11","_id":"8130","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-09-05T14:19:06Z","file_date_updated":"2020-12-02T08:50:38Z","department":[{"_id":"RoSe"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). I thank Stefan Teufel for helpful remarks and for his involvement in the closely related joint project [10]. Helpful discussions with Serena Cenatiempo and Nikolai Leopold are gratefully acknowledged. This work was supported by the German Research Foundation within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems” and has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Archive for Rational Mechanics and Analysis","day":"01","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-07-18T15:06:35Z","date_published":"2020-11-01T00:00:00Z","doi":"10.1007/s00205-020-01548-w","page":"541-606","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606.","chicago":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01548-w.","short":"L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606.","ieee":"L. Bossmann, “Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons,” Archive for Rational Mechanics and Analysis, vol. 238, no. 11. Springer Nature, pp. 541–606, 2020.","apa":"Bossmann, L. (2020). Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-020-01548-w","ama":"Bossmann L. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 2020;238(11):541-606. doi:10.1007/s00205-020-01548-w","mla":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis, vol. 238, no. 11, Springer Nature, 2020, pp. 541–606, doi:10.1007/s00205-020-01548-w."},"title":"Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1907.04547"],"isi":["000550164400001"]},"author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","last_name":"Bossmann","full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343"}]},{"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Lieb, Elliott H., and Robert Seiringer. “Divergence of the Effective Mass of a Polaron in the Strong Coupling Limit.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-019-02322-3.","ista":"Lieb EH, Seiringer R. 2020. Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. 180, 23–33.","mla":"Lieb, Elliott H., and Robert Seiringer. “Divergence of the Effective Mass of a Polaron in the Strong Coupling Limit.” Journal of Statistical Physics, vol. 180, Springer Nature, 2020, pp. 23–33, doi:10.1007/s10955-019-02322-3.","short":"E.H. Lieb, R. Seiringer, Journal of Statistical Physics 180 (2020) 23–33.","ieee":"E. H. Lieb and R. Seiringer, “Divergence of the effective mass of a polaron in the strong coupling limit,” Journal of Statistical Physics, vol. 180. Springer Nature, pp. 23–33, 2020.","apa":"Lieb, E. H., & Seiringer, R. (2020). Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-019-02322-3","ama":"Lieb EH, Seiringer R. Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. 2020;180:23-33. doi:10.1007/s10955-019-02322-3"},"title":"Divergence of the effective mass of a polaron in the strong coupling limit","author":[{"last_name":"Lieb","full_name":"Lieb, Elliott H.","first_name":"Elliott H."},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000556199700003"]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227; R.S.) is gratefully acknowledged.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Statistical Physics","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-09-01T00:00:00Z","doi":"10.1007/s10955-019-02322-3","date_created":"2020-01-07T09:42:03Z","page":"23-33","_id":"7235","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510","530"],"date_updated":"2023-09-05T14:57:29Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-11-19T11:13:55Z","oa_version":"Published Version","abstract":[{"text":"We consider the Fröhlich model of a polaron, and show that its effective mass diverges in thestrong coupling limit.","lang":"eng"}],"month":"09","intvolume":" 180","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2020-11-19T11:13:55Z","file_size":279749,"date_created":"2020-11-19T11:13:55Z","file_name":"2020_JourStatPhysics_Lieb.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8774","checksum":"1e67bee6728592f7bdcea2ad2d9366dc","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"publication_status":"published","volume":180,"ec_funded":1},{"oa_version":"Submitted Version","abstract":[{"text":"For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).\r\n\r\nFor Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.\r\n\r\nAs our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem.","lang":"eng"}],"intvolume":" 12107","month":"05","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/364"}],"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030457266","9783030457273"],"issn":["0302-9743"]},"ec_funded":1,"volume":12107,"_id":"7966","status":"public","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","end_date":"2020-05-15","start_date":"2020-05-11"},"type":"conference","date_updated":"2023-09-05T15:06:40Z","department":[{"_id":"KrPi"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Advances in Cryptology – EUROCRYPT 2020","day":"01","year":"2020","isi":1,"date_created":"2020-06-15T07:13:37Z","date_published":"2020-05-01T00:00:00Z","doi":"10.1007/978-3-030-45727-3_16","page":"475-506","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Auerbach, Benedikt, et al. “Everybody’s a Target: Scalability in Public-Key Encryption.” Advances in Cryptology – EUROCRYPT 2020, vol. 12107, Springer Nature, 2020, pp. 475–506, doi:10.1007/978-3-030-45727-3_16.","ieee":"B. Auerbach, F. Giacon, and E. Kiltz, “Everybody’s a target: Scalability in public-key encryption,” in Advances in Cryptology – EUROCRYPT 2020, 2020, vol. 12107, pp. 475–506.","short":"B. Auerbach, F. Giacon, E. Kiltz, in:, Advances in Cryptology – EUROCRYPT 2020, Springer Nature, 2020, pp. 475–506.","apa":"Auerbach, B., Giacon, F., & Kiltz, E. (2020). Everybody’s a target: Scalability in public-key encryption. In Advances in Cryptology – EUROCRYPT 2020 (Vol. 12107, pp. 475–506). Springer Nature. https://doi.org/10.1007/978-3-030-45727-3_16","ama":"Auerbach B, Giacon F, Kiltz E. Everybody’s a target: Scalability in public-key encryption. In: Advances in Cryptology – EUROCRYPT 2020. Vol 12107. Springer Nature; 2020:475-506. doi:10.1007/978-3-030-45727-3_16","chicago":"Auerbach, Benedikt, Federico Giacon, and Eike Kiltz. “Everybody’s a Target: Scalability in Public-Key Encryption.” In Advances in Cryptology – EUROCRYPT 2020, 12107:475–506. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45727-3_16.","ista":"Auerbach B, Giacon F, Kiltz E. 2020. Everybody’s a target: Scalability in public-key encryption. Advances in Cryptology – EUROCRYPT 2020. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 12107, 475–506."},"title":"Everybody’s a target: Scalability in public-key encryption","external_id":{"isi":["000828688000016"]},"article_processing_charge":"No","author":[{"first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt"},{"full_name":"Giacon, Federico","last_name":"Giacon","first_name":"Federico"},{"last_name":"Kiltz","full_name":"Kiltz, Eike","first_name":"Eike"}]},{"_id":"8623","type":"conference","conference":{"name":"RV: Runtime Verification","end_date":"2020-10-09","location":"Los Angeles, CA, United States","start_date":"2020-10-06"},"status":"public","date_updated":"2023-09-05T15:08:26Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-15T14:28:06Z","abstract":[{"lang":"eng","text":"We introduce the monitoring of trace properties under assumptions. An assumption limits the space of possible traces that the monitor may encounter. An assumption may result from knowledge about the system that is being monitored, about the environment, or about another, connected monitor. We define monitorability under assumptions and study its theoretical properties. In particular, we show that for every assumption A, the boolean combinations of properties that are safe or co-safe relative to A are monitorable under A. We give several examples and constructions on how an assumption can make a non-monitorable property monitorable, and how an assumption can make a monitorable property monitorable with fewer resources, such as integer registers."}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":"1","month":"10","intvolume":" 12399","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030605070","9783030605087"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"00661f9b7034f52e18bf24fa552b8194","file_id":"8665","creator":"esarac","file_size":478148,"date_updated":"2020-10-15T14:28:06Z","file_name":"monitorability.pdf","date_created":"2020-10-15T14:28:06Z"}],"language":[{"iso":"eng"}],"volume":12399,"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Henzinger, Thomas A, and Naci E Sarac. “Monitorability under Assumptions.” In Runtime Verification, 12399:3–18. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60508-7_1.","ista":"Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Monitorability under Assumptions.” Runtime Verification, vol. 12399, Springer Nature, 2020, pp. 3–18, doi:10.1007/978-3-030-60508-7_1.","ieee":"T. A. Henzinger and N. E. Sarac, “Monitorability under assumptions,” in Runtime Verification, Los Angeles, CA, United States, 2020, vol. 12399, pp. 3–18.","short":"T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020, pp. 3–18.","apa":"Henzinger, T. A., & Sarac, N. E. (2020). Monitorability under assumptions. In Runtime Verification (Vol. 12399, pp. 3–18). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-60508-7_1","ama":"Henzinger TA, Sarac NE. Monitorability under assumptions. In: Runtime Verification. Vol 12399. Springer Nature; 2020:3-18. doi:10.1007/978-3-030-60508-7_1"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"article_processing_charge":"No","external_id":{"isi":["000728160600001"]},"title":"Monitorability under assumptions","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"02","publication":"Runtime Verification","page":"3-18","doi":"10.1007/978-3-030-60508-7_1","date_published":"2020-10-02T00:00:00Z","date_created":"2020-10-07T15:05:37Z"},{"date_created":"2020-11-06T08:45:03Z","doi":"10.1007/978-3-030-60440-0_26","date_published":"2020-10-09T00:00:00Z","page":"325-338","publication":"Graph-Theoretic Concepts in Computer Science","day":"09","year":"2020","quality_controlled":"1","publisher":"Springer Nature","title":"Inserting one edge into a simple drawing is hard","article_processing_charge":"No","author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M"},{"first_name":"Fabian","full_name":"Klute, Fabian","last_name":"Klute"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"},{"last_name":"Seidel","full_name":"Seidel, Raimund","first_name":"Raimund"},{"first_name":"Birgit","last_name":"Vogtenhuber","full_name":"Vogtenhuber, Birgit"},{"full_name":"Wiedera, Tilo","last_name":"Wiedera","first_name":"Tilo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Graph-Theoretic Concepts in Computer Science, vol. 12301, Springer Nature, 2020, pp. 325–38, doi:10.1007/978-3-030-60440-0_26.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, R. Seidel, B. Vogtenhuber, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” in Graph-Theoretic Concepts in Computer Science, Leeds, United Kingdom, 2020, vol. 12301, pp. 325–338.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, R. Seidel, B. Vogtenhuber, T. Wiedera, in:, Graph-Theoretic Concepts in Computer Science, Springer Nature, 2020, pp. 325–338.","ama":"Arroyo Guevara AM, Klute F, Parada I, Seidel R, Vogtenhuber B, Wiedera T. Inserting one edge into a simple drawing is hard. In: Graph-Theoretic Concepts in Computer Science. Vol 12301. Springer Nature; 2020:325-338. doi:10.1007/978-3-030-60440-0_26","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Seidel, R., Vogtenhuber, B., & Wiedera, T. (2020). Inserting one edge into a simple drawing is hard. In Graph-Theoretic Concepts in Computer Science (Vol. 12301, pp. 325–338). Leeds, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-60440-0_26","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Raimund Seidel, Birgit Vogtenhuber, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” In Graph-Theoretic Concepts in Computer Science, 12301:325–38. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60440-0_26.","ista":"Arroyo Guevara AM, Klute F, Parada I, Seidel R, Vogtenhuber B, Wiedera T. 2020. Inserting one edge into a simple drawing is hard. Graph-Theoretic Concepts in Computer Science. WG: Workshop on Graph-Theoretic Concepts in Computer Science, LNCS, vol. 12301, 325–338."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ec_funded":1,"volume":12301,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030604394","9783030604400"],"eissn":["1611-3349"]},"intvolume":" 12301","month":"10","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"None","abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP -complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ , it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"department":[{"_id":"UlWa"}],"date_updated":"2023-09-05T15:09:16Z","status":"public","conference":{"name":"WG: Workshop on Graph-Theoretic Concepts in Computer Science","start_date":"2020-06-24","location":"Leeds, United Kingdom","end_date":"2020-06-26"},"type":"conference","_id":"8732"},{"volume":12110,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030453732","9783030453749"],"eissn":["1611-3349"]},"publication_status":"published","place":"Cham","month":"04","intvolume":" 12110","scopus_import":"1","main_file_link":[{"url":"https://eprint.iacr.org/2020/090","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce the notion of Witness Maps as a cryptographic notion of a proof system. A Unique Witness Map (UWM) deterministically maps all witnesses for an NP statement to a single representative witness, resulting in a computationally sound, deterministic-prover, non-interactive witness independent proof system. A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable” mode to a CWM.\r\nOur main construction is a DMWM for all NP relations, assuming sub-exponentially secure indistinguishability obfuscation ( iO ), along with standard cryptographic assumptions. The DMWM construction relies on a CWM and a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF), both of which are in turn instantiated based on iO and other primitives. Our instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct, from standard assumptions, Puncturable Digital Signatures and a new primitive called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially secure iO and sub-exponentially secure OWF.\r\nAs an application of our constructions, we show how to use a DMWM to construct the first leakage and tamper-resilient signatures with a deterministic signer, thereby solving a decade old open problem posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs (Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction achieves the optimal leakage rate of 1−o(1) ."}],"date_updated":"2023-09-05T15:10:02Z","status":"public","type":"book_chapter","series_title":"LNCS","_id":"10865","doi":"10.1007/978-3-030-45374-9_8","date_published":"2020-04-29T00:00:00Z","date_created":"2022-03-18T11:35:51Z","page":"220-246","day":"29","publication":"Public-Key Cryptography","year":"2020","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank the anonymous reviewers of PKC 2019 for their useful comments and suggestions. We thank Omer Paneth for pointing out to us the connection between Unique Witness Maps (UWM) and Witness encryption (WE). The first author would like to acknowledge Pandu Rangan for his involvement during the initial discussion phase of the project.","editor":[{"full_name":"Kiayias, A","last_name":"Kiayias","first_name":"A"}],"title":"Witness maps and applications","author":[{"last_name":"Chakraborty","full_name":"Chakraborty, Suvradip","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"first_name":"Manoj","full_name":"Prabhakaran, Manoj","last_name":"Prabhakaran"},{"first_name":"Daniel","last_name":"Wichs","full_name":"Wichs, Daniel"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications. In: Public-Key Cryptography. vol. 12110, 220–246.","chicago":"Chakraborty, Suvradip, Manoj Prabhakaran, and Daniel Wichs. “Witness Maps and Applications.” In Public-Key Cryptography, edited by A Kiayias, 12110:220–46. LNCS. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_8.","ama":"Chakraborty S, Prabhakaran M, Wichs D. Witness maps and applications. In: Kiayias A, ed. Public-Key Cryptography. Vol 12110. LNCS. Cham: Springer Nature; 2020:220-246. doi:10.1007/978-3-030-45374-9_8","apa":"Chakraborty, S., Prabhakaran, M., & Wichs, D. (2020). Witness maps and applications. In A. Kiayias (Ed.), Public-Key Cryptography (Vol. 12110, pp. 220–246). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_8","ieee":"S. Chakraborty, M. Prabhakaran, and D. Wichs, “Witness maps and applications,” in Public-Key Cryptography, vol. 12110, A. Kiayias, Ed. Cham: Springer Nature, 2020, pp. 220–246.","short":"S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key Cryptography, Springer Nature, Cham, 2020, pp. 220–246.","mla":"Chakraborty, Suvradip, et al. “Witness Maps and Applications.” Public-Key Cryptography, edited by A Kiayias, vol. 12110, Springer Nature, 2020, pp. 220–46, doi:10.1007/978-3-030-45374-9_8."}},{"_id":"7611","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-05T15:14:50Z","ddc":["510"],"file_date_updated":"2020-11-20T12:04:26Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"We consider a system of N bosons in the limit N→∞, interacting through singular potentials. For initial data exhibiting Bose–Einstein condensation, the many-body time evolution is well approximated through a quadratic fluctuation dynamics around a cubic nonlinear Schrödinger equation of the condensate wave function. We show that these fluctuations satisfy a (multi-variate) central limit theorem.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 110","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"publication_status":"published","file":[{"creator":"dernst","file_size":478683,"date_updated":"2020-11-20T12:04:26Z","file_name":"2020_LettersMathPhysics_Rademacher.pdf","date_created":"2020-11-20T12:04:26Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"3bdd41f10ad947b67a45b98f507a7d4a","file_id":"8784"}],"language":[{"iso":"eng"}],"volume":110,"ec_funded":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"citation":{"mla":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics, vol. 110, Springer Nature, 2020, pp. 2143–74, doi:10.1007/s11005-020-01286-w.","short":"S.A.E. Rademacher, Letters in Mathematical Physics 110 (2020) 2143–2174.","ieee":"S. A. E. Rademacher, “Central limit theorem for Bose gases interacting through singular potentials,” Letters in Mathematical Physics, vol. 110. Springer Nature, pp. 2143–2174, 2020.","ama":"Rademacher SAE. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 2020;110:2143-2174. doi:10.1007/s11005-020-01286-w","apa":"Rademacher, S. A. E. (2020). Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-020-01286-w","chicago":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” Letters in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s11005-020-01286-w.","ista":"Rademacher SAE. 2020. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 110, 2143–2174."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"}],"external_id":{"isi":["000551556000006"]},"article_processing_charge":"Yes (via OA deal)","title":"Central limit theorem for Bose gases interacting through singular potentials","acknowledgement":"Simone Rademacher acknowledges partial support from the NCCR SwissMAP. This project has received\r\nfunding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nS.R. would like to thank Benjamin Schlein for many fruitful discussions.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"12","publication":"Letters in Mathematical Physics","page":"2143-2174","doi":"10.1007/s11005-020-01286-w","date_published":"2020-03-12T00:00:00Z","date_created":"2020-03-23T11:11:47Z"},{"publisher":"Wiley","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Ecological Monographs","date_published":"2020-02-01T00:00:00Z","doi":"10.1002/ecm.1397","date_created":"2020-01-07T12:47:07Z","article_number":"e01397","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"citation":{"chicago":"Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs. Wiley, 2020. https://doi.org/10.1002/ecm.1397.","ista":"Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397.","mla":"Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs, vol. 90, no. 1, e01397, Wiley, 2020, doi:10.1002/ecm.1397.","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020).","ieee":"C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” Ecological Monographs, vol. 90, no. 1. Wiley, 2020.","apa":"Baskett, C., Schroeder, L., Weber, M. G., & Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. Wiley. https://doi.org/10.1002/ecm.1397","ama":"Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 2020;90(1). doi:10.1002/ecm.1397"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lucy","full_name":"Schroeder, Lucy","last_name":"Schroeder"},{"full_name":"Weber, Marjorie G.","last_name":"Weber","first_name":"Marjorie G."},{"full_name":"Schemske, Douglas W.","last_name":"Schemske","first_name":"Douglas W."}],"external_id":{"isi":["000508511600001"]},"article_processing_charge":"Yes (via OA deal)","title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","abstract":[{"text":"The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 90","publication_identifier":{"issn":["0012-9615"],"eissn":["1557-7015"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7469","checksum":"ab8130c6e68101f5a091d05324c36f08","creator":"dernst","date_updated":"2020-07-14T12:47:54Z","file_size":537941,"date_created":"2020-02-10T08:18:14Z","file_name":"2020_EcologMono_Baskett.pdf"}],"language":[{"iso":"eng"}],"issue":"1","volume":90,"license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"_id":"7236","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","date_updated":"2023-09-05T15:43:19Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"NiBa"}]},{"issue":"5","volume":227,"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8799","checksum":"8e8150dbbba8cb65b72f81d1f0864b8b","success":1,"creator":"dernst","date_updated":"2020-11-24T12:19:38Z","file_size":3643395,"date_created":"2020-11-24T12:19:38Z","file_name":"2020_09_NewPhytologist_Zhang.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"publication_status":"published","month":"09","intvolume":" 227","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.\r\n* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.\r\n* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.\r\n* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants."}],"file_date_updated":"2020-11-24T12:19:38Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-09-05T15:46:04Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7697","doi":"10.1111/nph.16629","date_published":"2020-09-01T00:00:00Z","date_created":"2020-04-30T08:43:29Z","page":"1406-1416","day":"01","publication":"New Phytologist","has_accepted_license":"1","isi":1,"year":"2020","publisher":"Wiley","quality_controlled":"1","oa":1,"title":"Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters","author":[{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang"},{"last_name":"Hartinger","full_name":"Hartinger, Corinna","orcid":"0000-0003-1618-2737","first_name":"Corinna","id":"AEFB2266-8ABF-11EA-AA39-812C3623CBE4"},{"first_name":"Xiaojuan","full_name":"Wang, Xiaojuan","last_name":"Wang"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["32350870"],"isi":["000534092400001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Zhang Y, Hartinger C, Wang X, Friml J. 2020. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 227(5), 1406–1416.","chicago":"Zhang, Yuzhou, Corinna Hartinger, Xiaojuan Wang, and Jiří Friml. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16629.","short":"Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416.","ieee":"Y. Zhang, C. Hartinger, X. Wang, and J. Friml, “Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters,” New Phytologist, vol. 227, no. 5. Wiley, pp. 1406–1416, 2020.","apa":"Zhang, Y., Hartinger, C., Wang, X., & Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. Wiley. https://doi.org/10.1111/nph.16629","ama":"Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 2020;227(5):1406-1416. doi:10.1111/nph.16629","mla":"Zhang, Yuzhou, et al. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” New Phytologist, vol. 227, no. 5, Wiley, 2020, pp. 1406–16, doi:10.1111/nph.16629."},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"page":"89-99","date_published":"2020-05-01T00:00:00Z","doi":"10.1111/cgf.13914","date_created":"2020-11-17T09:35:10Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Computer Graphics Forum","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176.","author":[{"last_name":"Schreck","full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"external_id":{"isi":["000548709600008"]},"article_processing_charge":"No","title":"A practical method for animating anisotropic elastoplastic materials","citation":{"chicago":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.13914.","ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","mla":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” Computer Graphics Forum, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:10.1111/cgf.13914.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99.","ieee":"C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” Computer Graphics Forum, vol. 39, no. 2. Wiley, pp. 89–99, 2020.","apa":"Schreck, C., & Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13914","ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 2020;39(2):89-99. doi:10.1111/cgf.13914"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"issue":"2","volume":39,"ec_funded":1,"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-11-23T09:05:13Z","file_size":38969122,"date_created":"2020-11-23T09:05:13Z","file_name":"2020_poff_revisited.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7605f605acd84d0942b48bc7a1c2d72e","file_id":"8796","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 39","abstract":[{"lang":"eng","text":"This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","file_date_updated":"2020-11-23T09:05:13Z","department":[{"_id":"ChWo"}],"date_updated":"2023-09-05T16:00:13Z","ddc":["000"],"article_type":"original","type":"journal_article","status":"public","keyword":["Computer Networks and Communications"],"_id":"8765"},{"citation":{"ista":"Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 132(37), 16047–16051.","chicago":"Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Frederic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie. Wiley, 2020. https://doi.org/10.1002/ange.202005378.","ieee":"R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie, vol. 132, no. 37. Wiley, pp. 16047–16051, 2020.","short":"R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie 132 (2020) 16047–16051.","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202005378","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 2020;132(37):16047-16051. doi:10.1002/ange.202005378","mla":"Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie, vol. 132, no. 37, Wiley, 2020, pp. 16047–51, doi:10.1002/ange.202005378."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Bouchal","full_name":"Bouchal, Roza","first_name":"Roza"},{"last_name":"Li","full_name":"Li, Zhujie","first_name":"Zhujie"},{"first_name":"Chandra","full_name":"Bongu, Chandra","last_name":"Bongu"},{"first_name":"Steven","full_name":"Le Vot, Steven","last_name":"Le Vot"},{"first_name":"Romain","full_name":"Berthelot, Romain","last_name":"Berthelot"},{"first_name":"Benjamin","last_name":"Rotenberg","full_name":"Rotenberg, Benjamin"},{"full_name":"Favier, Frederic","last_name":"Favier","first_name":"Frederic"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"first_name":"Mathieu","full_name":"Salanne, Mathieu","last_name":"Salanne"},{"first_name":"Olivier","full_name":"Fontaine, Olivier","last_name":"Fontaine"}],"title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2020","has_accepted_license":"1","publication":"Angewandte Chemie","day":"07","page":"16047-16051","date_created":"2020-06-29T16:15:49Z","doi":"10.1002/ange.202005378","date_published":"2020-09-07T00:00:00Z","_id":"8057","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-05T15:47:50Z","ddc":["540","541"],"department":[{"_id":"StFr"}],"file_date_updated":"2020-09-17T08:59:43Z","abstract":[{"lang":"eng","text":"Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 132","month":"09","publication_status":"published","publication_identifier":{"issn":["0044-8249"],"eissn":["1521-3757"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8401","checksum":"7dd0a56f6bd5de08ea75b1ec388c91bc","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_AngChemieDE_Bouchal.pdf","date_created":"2020-09-17T08:59:43Z","creator":"dernst","file_size":1904552,"date_updated":"2020-09-17T08:59:43Z"}],"volume":132,"issue":"37"},{"acknowledgement":"We thank Bernhardt Steinwender and Jorgen Eilenberg for the fungal strains, Xavier Espadaler, Mireia Diaz, Christiane Wanke, Lumi Viljakainen and the Social Immunity Team at IST Austria, for help with ant collection, and Wanda Gorecka and Gertraud Stift of the IST Austria Life Science Facility for technical support. We are thankful to Dieter Ebert for input at all stages of the project, Roger Mundry for statistical advice, Hinrich Schulenburg, Paul Schmid-Hempel, Yuko\r\nUlrich and Joachim Kurtz for project discussion, Bor Kavcic for advice on growth curves, Marcus Roper for advice on modelling work and comments on the manuscript, as well as Marjon de Vos, Weini Huang and the Social Immunity Team for comments on the manuscript.\r\nThis study was funded by the German Research Foundation (DFG) within the Priority Programme 1399 Host-parasite Coevolution (CR 118/3 to S.C.) and the People Programme\r\n(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no 291734 (ISTFELLOW to B.M.). ","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"Ecology Letters","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-03-01T00:00:00Z","doi":"10.1111/ele.13458","date_created":"2020-01-20T13:32:12Z","page":"565-574","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13458","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 2020;23(3):565-574. doi:10.1111/ele.13458","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 565–574, 2020.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, Ecology Letters 23 (2020) 565–574.","mla":"Milutinovic, Barbara, et al. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 565–74, doi:10.1111/ele.13458.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 23(3), 565–574.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13458."},"title":"Social immunity modulates competition between coinfecting pathogens","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic"},{"full_name":"Stock, Miriam","last_name":"Stock","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000507515900001"]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level.","lang":"eng"}],"month":"03","intvolume":" 23","scopus_import":"1","file":[{"file_id":"8776","checksum":"0cd8be386fa219db02845b7c3991ce04","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-11-19T11:27:10Z","file_name":"2020_EcologyLetters_Milutinovic.pdf","date_updated":"2020-11-19T11:27:10Z","file_size":561749,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1461-0248"],"issn":["1461-023X"]},"publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"13060","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/social-ants-shapes-disease-outcome/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"3","volume":23,"ec_funded":1,"_id":"7343","status":"public","article_type":"letter_note","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"ddc":["570"],"date_updated":"2023-09-05T16:04:49Z","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"file_date_updated":"2020-11-19T11:27:10Z"},{"publication":"Molecular Ecology Resources","day":"01","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-07-07T08:56:16Z","date_published":"2020-11-01T00:00:00Z","doi":"10.1111/1755-0998.13210","page":"1517-1525","oa":1,"publisher":"Wiley","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525. doi:10.1111/1755-0998.13210","apa":"Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13210","ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from sex chromosomes,” Molecular Ecology Resources, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:10.1111/1755-0998.13210.","ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources. Wiley, 2020. https://doi.org/10.1111/1755-0998.13210."},"title":"Disagreement in FST estimators: A case study from sex chromosomes","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["32543001"],"isi":["000545451200001"]},"author":[{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","full_name":"Gammerdinger, William J","last_name":"Gammerdinger"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"language":[{"iso":"eng"}],"file":[{"checksum":"3d87ebb8757dcd504f20c618b72e6575","file_id":"8814","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-11-26T11:46:43Z","file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","date_updated":"2020-11-26T11:46:43Z","file_size":820428,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"ec_funded":1,"volume":20,"issue":"6","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses."}],"intvolume":" 20","month":"11","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-05T16:07:08Z","file_date_updated":"2020-11-26T11:46:43Z","department":[{"_id":"BeVi"}],"_id":"8099","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","author":[{"first_name":"Roza","full_name":"Bouchal, Roza","last_name":"Bouchal"},{"first_name":"Zhujie","last_name":"Li","full_name":"Li, Zhujie"},{"full_name":"Bongu, Chandra","last_name":"Bongu","first_name":"Chandra"},{"first_name":"Steven","last_name":"Le Vot","full_name":"Le Vot, Steven"},{"first_name":"Romain","last_name":"Berthelot","full_name":"Berthelot, Romain"},{"last_name":"Rotenberg","full_name":"Rotenberg, Benjamin","first_name":"Benjamin"},{"first_name":"Fréderic","full_name":"Favier, Fréderic","last_name":"Favier"},{"last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Mathieu","full_name":"Salanne, Mathieu","last_name":"Salanne"},{"first_name":"Olivier","full_name":"Fontaine, Olivier","last_name":"Fontaine"}],"external_id":{"pmid":["32390281"],"isi":["000541488700001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Fréderic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202005378.","ista":"Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 59(37), 15913–1591.","mla":"Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” Angewandte Chemie International Edition, vol. 59, no. 37, Wiley, 2020, pp. 15913–1591, doi:10.1002/anie.202005378.","short":"R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie International Edition 59 (2020) 15913–1591.","ieee":"R. Bouchal et al., “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” Angewandte Chemie International Edition, vol. 59, no. 37. Wiley, pp. 15913–1591, 2020.","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 2020;59(37):15913-1591. doi:10.1002/anie.202005378","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202005378"},"quality_controlled":"1","publisher":"Wiley","oa":1,"doi":"10.1002/anie.202005378","date_published":"2020-09-07T00:00:00Z","date_created":"2020-05-14T21:00:30Z","page":"15913-1591","day":"07","publication":"Angewandte Chemie International Edition","isi":1,"has_accepted_license":"1","year":"2020","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7847","department":[{"_id":"StFr"}],"file_date_updated":"2020-09-17T08:57:16Z","ddc":["540","546"],"date_updated":"2023-09-05T16:02:53Z","month":"09","intvolume":" 59","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities nearing 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of 'free' and 'bound' water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability. "}],"issue":"37","volume":59,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"7b6c2fc20e9b0ff4353352f7a7004e2d","file_id":"8400","creator":"dernst","file_size":1966184,"date_updated":"2020-09-17T08:57:16Z","file_name":"2020_AngChemieINT_Buchal.pdf","date_created":"2020-09-17T08:57:16Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publication_status":"published"},{"citation":{"mla":"Rybicki, Joel, et al. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 506–17, doi:10.1111/ele.13450.","short":"J. Rybicki, N. Abrego, O. Ovaskainen, Ecology Letters 23 (2020) 506–517.","ieee":"J. Rybicki, N. Abrego, and O. Ovaskainen, “Habitat fragmentation and species diversity in competitive communities,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 506–517, 2020.","apa":"Rybicki, J., Abrego, N., & Ovaskainen, O. (2020). Habitat fragmentation and species diversity in competitive communities. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13450","ama":"Rybicki J, Abrego N, Ovaskainen O. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 2020;23(3):506-517. doi:10.1111/ele.13450","chicago":"Rybicki, Joel, Nerea Abrego, and Otso Ovaskainen. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13450.","ista":"Rybicki J, Abrego N, Ovaskainen O. 2020. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 23(3), 506–517."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000503625200001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nerea","last_name":"Abrego","full_name":"Abrego, Nerea"},{"full_name":"Ovaskainen, Otso","last_name":"Ovaskainen","first_name":"Otso"}],"title":"Habitat fragmentation and species diversity in competitive communities","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","grant_number":"840605"}],"year":"2020","isi":1,"has_accepted_license":"1","publication":"Ecology Letters","day":"01","page":"506-517","date_created":"2020-01-04T11:04:30Z","doi":"10.1111/ele.13450","date_published":"2020-03-01T00:00:00Z","oa":1,"publisher":"Wiley","quality_controlled":"1","date_updated":"2023-09-05T16:04:30Z","ddc":["000"],"department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:47:54Z","_id":"7224","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1461-0248"],"issn":["1461-023X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"372f67f2744f4b6049e9778364766c22","file_id":"7486","file_size":3005474,"date_updated":"2020-07-14T12:47:54Z","creator":"dernst","file_name":"2020_EcologyLetters_Rybicki.pdf","date_created":"2020-02-14T12:02:50Z"}],"ec_funded":1,"volume":23,"issue":"3","abstract":[{"lang":"eng","text":"Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 23","month":"03"},{"title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries","external_id":{"isi":["000576148700001"]},"article_processing_charge":"No","author":[{"first_name":"Werner","full_name":"Schlemmer, Werner","last_name":"Schlemmer"},{"first_name":"Philipp","last_name":"Nothdurft","full_name":"Nothdurft, Philipp"},{"first_name":"Alina","last_name":"Petzold","full_name":"Petzold, Alina"},{"first_name":"Philipp","last_name":"Frühwirt","full_name":"Frühwirt, Philipp"},{"last_name":"Schmallegger","full_name":"Schmallegger, Max","first_name":"Max"},{"full_name":"Gescheidt-Demner, Georg","last_name":"Gescheidt-Demner","first_name":"Georg"},{"first_name":"Roland","full_name":"Fischer, Roland","last_name":"Fischer"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"full_name":"Kern, Wolfgang","last_name":"Kern","first_name":"Wolfgang"},{"first_name":"Stefan","last_name":"Spirk","full_name":"Spirk, Stefan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253.","ieee":"W. Schlemmer et al., “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” Angewandte Chemie International Edition, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020.","short":"W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946.","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202008253","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 2020;59(51):22943-22946. doi:10.1002/anie.202008253","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger, Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202008253.","ista":"Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 59(51), 22943–22946."},"date_created":"2020-09-03T16:10:56Z","date_published":"2020-12-14T00:00:00Z","doi":"10.1002/anie.202008253","page":"22943-22946","publication":"Angewandte Chemie International Edition","day":"14","year":"2020","isi":1,"oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","department":[{"_id":"StFr"}],"date_updated":"2023-09-05T16:03:47Z","status":"public","type":"journal_article","article_type":"original","_id":"8329","issue":"51","volume":59,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9780"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"intvolume":" 59","month":"12","main_file_link":[{"url":"https://doi.org/10.1002/anie.202008253","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles."}]},{"status":"public","type":"research_data_reference","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)"},"_id":"13060","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"title":"Social immunity modulates competition between coinfecting pathogens","author":[{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758"},{"first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","full_name":"Stock, Miriam"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318.","mla":"Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318.","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020)."},"date_updated":"2023-09-05T16:04:48Z","month":"12","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.crjdfn318"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level."}],"doi":"10.5061/DRYAD.CRJDFN318","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7343"}]},"date_published":"2020-12-19T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:11:22Z","day":"19","year":"2020"},{"type":"research_data_reference","status":"public","_id":"9780","author":[{"first_name":"Werner","last_name":"Schlemmer","full_name":"Schlemmer, Werner"},{"first_name":"Philipp","last_name":"Nothdurft","full_name":"Nothdurft, Philipp"},{"last_name":"Petzold","full_name":"Petzold, Alina","first_name":"Alina"},{"first_name":"Gisbert","last_name":"Riess","full_name":"Riess, Gisbert"},{"full_name":"Frühwirt, Philipp","last_name":"Frühwirt","first_name":"Philipp"},{"full_name":"Schmallegger, Max","last_name":"Schmallegger","first_name":"Max"},{"first_name":"Georg","last_name":"Gescheidt-Demner","full_name":"Gescheidt-Demner, Georg"},{"first_name":"Roland","last_name":"Fischer","full_name":"Fischer, Roland"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"},{"first_name":"Wolfgang","last_name":"Kern","full_name":"Kern, Wolfgang"},{"first_name":"Stefan","full_name":"Spirk, Stefan","last_name":"Spirk"}],"article_processing_charge":"No","department":[{"_id":"StFr"}],"title":"CCDC 1991959: Experimental Crystal Structure Determination","date_updated":"2023-09-05T16:03:47Z","citation":{"mla":"Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure Determination. CCDC, 2020, doi:10.5517/ccdc.csd.cc24vsrk.","short":"W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020).","ieee":"W. Schlemmer et al., “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.","ista":"Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, 10.5517/ccdc.csd.cc24vsrk."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"CCDC","main_file_link":[{"url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk","open_access":"1"}],"oa":1,"month":"03","abstract":[{"lang":"eng","text":"PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","id":"8329","status":"public"}]},"doi":"10.5517/ccdc.csd.cc24vsrk","date_published":"2020-03-22T00:00:00Z","date_created":"2021-08-06T07:41:07Z","year":"2020","day":"22"},{"project":[{"grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425"},{"_id":"26436750-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"785907","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)"}],"title":"Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease","author":[{"last_name":"Martín-Belmonte","full_name":"Martín-Belmonte, Alejandro","first_name":"Alejandro"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"first_name":"Rocío","full_name":"Alfaro-Ruíz, Rocío","last_name":"Alfaro-Ruíz"},{"full_name":"Moreno-Martínez, Ana Esther","last_name":"Moreno-Martínez","first_name":"Ana Esther"},{"last_name":"De La Ossa","full_name":"De La Ossa, Luis","first_name":"Luis"},{"first_name":"José","full_name":"Martínez-Hernández, José","last_name":"Martínez-Hernández"},{"first_name":"Alain","last_name":"Buisson","full_name":"Buisson, Alain"},{"last_name":"Früh","full_name":"Früh, Simon","first_name":"Simon"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"last_name":"Luján","full_name":"Luján, Rafael","first_name":"Rafael"}],"article_processing_charge":"No","external_id":{"isi":["000502270900001"],"pmid":["31729777"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Früh S, Bettler B, Shigemoto R, Fukazawa Y, Luján R. 2020. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 30(3), 554–575.","chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology. Wiley, 2020. https://doi.org/10.1111/bpa.12802.","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. Wiley. https://doi.org/10.1111/bpa.12802","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 2020;30(3):554-575. doi:10.1111/bpa.12802","short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, S. Früh, B. Bettler, R. Shigemoto, Y. Fukazawa, R. Luján, Brain Pathology 30 (2020) 554–575.","ieee":"A. Martín-Belmonte et al., “Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease,” Brain Pathology, vol. 30, no. 3. Wiley, pp. 554–575, 2020.","mla":"Martín-Belmonte, Alejandro, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology, vol. 30, no. 3, Wiley, 2020, pp. 554–75, doi:10.1111/bpa.12802."},"publisher":"Wiley","quality_controlled":"1","oa":1,"date_published":"2020-05-01T00:00:00Z","doi":"10.1111/bpa.12802","date_created":"2019-12-22T23:00:43Z","page":"554-575","day":"01","publication":"Brain Pathology","isi":1,"has_accepted_license":"1","year":"2020","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7207","department":[{"_id":"RySh"}],"file_date_updated":"2020-09-22T09:47:19Z","ddc":["570"],"date_updated":"2023-09-06T14:48:01Z","month":"05","intvolume":" 30","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD.","lang":"eng"}],"issue":"3","volume":30,"ec_funded":1,"file":[{"success":1,"file_id":"8554","checksum":"549cc1b18f638a21d17a939ba5563fa9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_BrainPathology_MartinBelmonte.pdf","date_created":"2020-09-22T09:47:19Z","creator":"dernst","file_size":4220935,"date_updated":"2020-09-22T09:47:19Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10156305"],"eissn":["17503639"]},"publication_status":"published"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2019-12-22T23:00:43Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1111/jeb.13570","page":"342-351","publication":"Journal of Evolutionary Biology","day":"01","year":"2020","has_accepted_license":"1","isi":1,"title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","external_id":{"isi":["000500954800001"],"pmid":["31724256"]},"article_processing_charge":"No","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka","first_name":"Zuzanna"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351.","mla":"Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570.","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570"},"intvolume":" 33","month":"03","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"13067","status":"public"}]},"volume":33,"issue":"3","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7534ff0839709c0c5265c12d29432f03","file_id":"8553","success":1,"creator":"dernst","date_updated":"2020-09-22T09:42:18Z","file_size":885611,"date_created":"2020-09-22T09:42:18Z","file_name":"2020_EvolBiology_Johannesson.pdf"}],"publication_status":"published","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7205","file_date_updated":"2020-09-22T09:42:18Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2023-09-06T14:48:57Z"},{"abstract":[{"text":"Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation.","lang":"eng"}],"oa_version":"None","pmid":1,"alternative_title":["Current Topics in Developmental Biology"],"scopus_import":"1","month":"06","intvolume":" 136","publication_identifier":{"issn":["00702153"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":136,"ec_funded":1,"_id":"7227","type":"book_chapter","status":"public","date_updated":"2023-09-06T14:54:36Z","department":[{"_id":"CaHe"}],"acknowledgement":"We thank Alexandra Schauer, Nicoletta Petridou and Feyza Nur Arslan for comments on the manuscript. Research in the Heisenberg laboratory is supported by an ERC Advanced Grant (MECSPEC 742573), ANR/FWF (I03601) and FWF/DFG (I03196) International Cooperation Grants. D. Pinheiro acknowledges a fellowship from EMBO ALTF (850-2017) and is currently supported by HFSP LTF (LT000429/2018-L2).","publisher":"Elsevier","quality_controlled":"1","isi":1,"year":"2020","day":"01","publication":"Gastrulation: From Embryonic Pattern to Form","page":"343-375","date_published":"2020-06-01T00:00:00Z","doi":"10.1016/bs.ctdb.2019.10.009","date_created":"2020-01-05T23:00:46Z","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of embryonic cleavage pattern","grant_number":"I03601"},{"grant_number":"I03196","name":"Control of epithelial cell layer spreading in zebrafish","call_identifier":"FWF","_id":"2608FC64-B435-11E9-9278-68D0E5697425"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"},{"grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Nunes Pinheiro, Diana C., and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–75, doi:10.1016/bs.ctdb.2019.10.009.","ieee":"D. C. Nunes Pinheiro and C.-P. J. Heisenberg, “Zebrafish gastrulation: Putting fate in motion,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, Elsevier, 2020, pp. 343–375.","short":"D.C. Nunes Pinheiro, C.-P.J. Heisenberg, in:, Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 343–375.","apa":"Nunes Pinheiro, D. C., & Heisenberg, C.-P. J. (2020). Zebrafish gastrulation: Putting fate in motion. In Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 343–375). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.10.009","ama":"Nunes Pinheiro DC, Heisenberg C-PJ. Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Vol 136. Elsevier; 2020:343-375. doi:10.1016/bs.ctdb.2019.10.009","chicago":"Nunes Pinheiro, Diana C, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation: Putting Fate in Motion.” In Gastrulation: From Embryonic Pattern to Form, 136:343–75. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.10.009.","ista":"Nunes Pinheiro DC, Heisenberg C-PJ. 2020.Zebrafish gastrulation: Putting fate in motion. In: Gastrulation: From Embryonic Pattern to Form. Current Topics in Developmental Biology, vol. 136, 343–375."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"pmid":["31959295"],"isi":["000611830600013"]},"title":"Zebrafish gastrulation: Putting fate in motion"},{"title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","article_processing_charge":"No","external_id":{"isi":["000494907500001"],"pmid":["31696770"]},"author":[{"first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","last_name":"Sinclair"},{"first_name":"S.","full_name":"Gille, S.","last_name":"Gille"},{"first_name":"M.","full_name":"Pauly, M.","last_name":"Pauly"},{"last_name":"Krämer","full_name":"Krämer, U.","first_name":"U."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Sinclair, S. A., Gille, S., Pauly, M., & Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. Informa UK Limited. https://doi.org/10.1080/15592324.2019.1687185","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687185","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling & Behavior 15 (2020).","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” Plant Signaling & Behavior, vol. 15, no. 1. Informa UK Limited, 2020.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:10.1080/15592324.2019.1687185.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 15(1), e1687185.","chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior. Informa UK Limited, 2020. https://doi.org/10.1080/15592324.2019.1687185."},"article_number":"e1687185","date_created":"2020-01-30T10:14:14Z","doi":"10.1080/15592324.2019.1687185","date_published":"2020-01-01T00:00:00Z","publication":"Plant Signaling & Behavior","day":"01","year":"2020","isi":1,"oa":1,"publisher":"Informa UK Limited","quality_controlled":"1","department":[{"_id":"JiFr"}],"date_updated":"2023-09-06T15:23:04Z","status":"public","type":"journal_article","article_type":"original","_id":"7417","volume":15,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"intvolume":" 15","month":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development.","lang":"eng"}]},{"ddc":["530","510"],"date_updated":"2023-09-07T12:54:12Z","file_date_updated":"2020-11-18T11:14:37Z","department":[{"_id":"LaEr"}],"_id":"6185","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2020-11-18T11:14:37Z","file_name":"2020_CommMathPhysics_Erdoes.pdf","date_updated":"2020-11-18T11:14:37Z","file_size":2904574,"creator":"dernst","checksum":"c3a683e2afdcea27afa6880b01e53dc2","file_id":"8771","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"6179","status":"public"}]},"volume":378,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).","lang":"eng"}],"month":"09","intvolume":" 378","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278.","chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03657-4.","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278.","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” Communications in Mathematical Physics, vol. 378. Springer Nature, pp. 1203–1278, 2020.","ama":"Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 2020;378:1203-1278. doi:10.1007/s00220-019-03657-4","apa":"Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03657-4","mla":"Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:10.1007/s00220-019-03657-4."},"title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000529483000001"],"arxiv":["1809.03971"]},"article_processing_charge":"Yes (via OA deal)","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"day":"01","publication":"Communications in Mathematical Physics","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1007/s00220-019-03657-4","date_published":"2020-09-01T00:00:00Z","date_created":"2019-03-28T10:21:15Z","page":"1203-1278","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work.","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"abstract":[{"text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"7657","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_PDFA.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:01Z","file_size":3297129},{"creator":"dernst","file_size":1063908,"date_updated":"2020-07-14T12:48:01Z","file_name":"Thesis_Forkert_source.zip","date_created":"2020-04-14T10:47:59Z","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","file_id":"7658"}],"language":[{"iso":"eng"}],"ec_funded":1,"_id":"7629","type":"dissertation","status":"public","supervisor":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"}],"date_updated":"2023-09-07T13:03:12Z","ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:48:01Z","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2020","day":"31","page":"154","doi":"10.15479/AT:ISTA:7629","date_published":"2020-03-31T00:00:00Z","date_created":"2020-04-02T06:40:23Z","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"citation":{"chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","last_name":"Forkert","full_name":"Forkert, Dominik L"}],"article_processing_charge":"No","title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains"},{"status":"public","type":"dissertation","_id":"8574","department":[{"_id":"NiBa"}],"file_date_updated":"2020-09-28T07:25:37Z","ddc":["570"],"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:11:39Z","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8575","checksum":"20e71f015fbbd78fea708893ad634ed0","creator":"dernst","file_size":6354833,"date_updated":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf","date_created":"2020-09-28T07:25:35Z"},{"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_id":"8576","checksum":"a8de2c14a1bb4e53c857787efbb289e1","date_updated":"2020-09-28T07:25:37Z","file_size":23020401,"creator":"dernst","date_created":"2020-09-28T07:25:37Z","file_name":"thesisFiles_EnikoSzep.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","title":"Local adaptation in metapopulations","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574."},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2020-09-20T00:00:00Z","doi":"10.15479/AT:ISTA:8574","date_created":"2020-09-28T07:33:38Z","page":"158","day":"20","has_accepted_license":"1","year":"2020"},{"ec_funded":1,"related_material":{"record":[{"id":"7524","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":1563429,"date_created":"2020-02-24T09:15:06Z","file_name":"thesis.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","file_id":"7515"},{"file_id":"7516","checksum":"ad7425867b52d7d9e72296e87bc9cb67","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2020-02-24T09:15:16Z","file_name":"thesis_source.zip","creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":2028038}],"alternative_title":["ISTA Thesis"],"month":"02","abstract":[{"text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:59Z","date_updated":"2023-09-07T13:12:42Z","supervisor":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"7514","page":"148","date_created":"2020-02-24T09:17:27Z","date_published":"2020-02-24T00:00:00Z","doi":"10.15479/AT:ISTA:7514","year":"2020","has_accepted_license":"1","day":"24","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"full_name":"Mayer, Simon","last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"title":"The free energy of a dilute two-dimensional Bose gas","citation":{"short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}]},{"related_material":{"record":[{"id":"8284","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-09-09T14:22:35Z","file_name":"Thesis_Julia_Steiner_pdfA.pdf","creator":"jsteiner","date_updated":"2021-09-16T12:40:56Z","file_size":117547589,"checksum":"2388d7e6e7a4d364c096fa89f305c3de","file_id":"8354","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"checksum":"ba112f957b7145462d0ab79044873ee9","file_id":"8355","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2020-09-09T14:23:25Z","file_name":"Thesis_Julia_Steiner.docx","creator":"jsteiner","date_updated":"2020-09-15T08:48:37Z","file_size":223328668}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"None","abstract":[{"text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"file_date_updated":"2021-09-16T12:40:56Z","department":[{"_id":"LeSa"}],"ddc":["572"],"date_updated":"2023-09-07T13:14:09Z","supervisor":[{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"dissertation","_id":"8353","date_created":"2020-09-09T14:27:01Z","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8353","page":"191","day":"09","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","article_processing_charge":"No","author":[{"last_name":"Steiner","orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia","first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353"},"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","page":"164","date_created":"2020-09-30T14:50:51Z","date_published":"2020-09-30T00:00:00Z","doi":"10.15479/AT:ISTA:8589","year":"2020","has_accepted_license":"1","day":"30","article_processing_charge":"No","author":[{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin"}],"title":"Novel insights into PIN polarity regulation during Arabidopsis development","citation":{"mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","related_material":{"record":[{"id":"7643","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8590","checksum":"c4bda1947d4c09c428ac9ce667b02327","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2020-09-30T14:50:20Z","file_name":"2020_Han_Thesis.docx","creator":"dernst","date_updated":"2020-09-30T14:50:20Z","file_size":49198118},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","file_id":"8591","file_size":15513963,"date_updated":"2021-10-01T13:33:02Z","creator":"dernst","file_name":"2020_Han_Thesis.pdf","date_created":"2020-09-30T14:49:59Z"}],"type":"dissertation","status":"public","_id":"8589","file_date_updated":"2021-10-01T13:33:02Z","department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T13:13:05Z","supervisor":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"ddc":["580"]},{"language":[{"iso":"eng"}],"file":[{"file_size":7320493,"date_updated":"2020-08-24T13:31:53Z","creator":"cziletti","file_name":"2020_eLife_Steiner.pdf","date_created":"2020-08-24T13:31:53Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","file_id":"8289"}],"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"volume":9,"related_material":{"record":[{"relation":"dissertation_contains","id":"8353","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release","description":"News on IST Homepage"}]},"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements."}],"intvolume":" 9","month":"07","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-07T13:14:08Z","department":[{"_id":"LeSa"}],"file_date_updated":"2020-08-24T13:31:53Z","_id":"8284","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","publication":"eLife","day":"31","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-08-24T06:24:04Z","doi":"10.7554/eLife.59407","date_published":"2020-07-31T00:00:00Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407.","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407","chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407.","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407."},"title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","external_id":{"pmid":["32735215"],"isi":["000562123600001"]},"article_processing_charge":"No","author":[{"orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia","last_name":"Steiner","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"article_number":"e59407","project":[{"grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","_id":"26169496-B435-11E9-9278-68D0E5697425"}]},{"oa_version":"Published Version","abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"month":"07","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"creator":"rgrah","file_size":16638998,"date_updated":"2020-07-27T12:00:07Z","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","date_created":"2020-07-27T12:00:07Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8176"},{"file_size":347459978,"date_updated":"2020-07-30T13:04:55Z","creator":"rgrah","file_name":"Thesis_new.zip","date_created":"2020-07-27T12:02:23Z","content_type":"application/zip","relation":"main_file","access_level":"closed","file_id":"8177"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"7675","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7569"},{"status":"public","id":"7652","relation":"part_of_dissertation"}]},"_id":"8155","status":"public","type":"dissertation","ddc":["530","570"],"date_updated":"2023-09-07T13:13:27Z","supervisor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-30T13:04:55Z","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"24","year":"2020","has_accepted_license":"1","date_created":"2020-07-23T09:51:28Z","date_published":"2020-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:8155","page":"310","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155."},"title":"Gene regulation across scales – how biophysical constraints shape evolution","article_processing_charge":"No","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"}]},{"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"citation":{"ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40.","chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212.","ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40. doi:10.1104/pp.20.00212","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212","ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” Plant Physiology, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rakusova, Hana","last_name":"Rakusova","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"external_id":{"isi":["000536641800018"],"pmid":["32107280"]},"article_processing_charge":"No","title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). ","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"isi":1,"year":"2020","day":"08","publication":"Plant Physiology","page":"37-40","date_published":"2020-05-08T00:00:00Z","doi":"10.1104/pp.20.00212","date_created":"2020-04-06T10:06:40Z","_id":"7643","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2023-09-07T13:13:04Z","department":[{"_id":"JiFr"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.20.00212"}],"month":"05","intvolume":" 183","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"8589","relation":"dissertation_contains"}]},"issue":"5","volume":183,"ec_funded":1},{"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Normative models of enhancer function","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T13:13:26Z","citation":{"mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405."},"status":"public","project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"type":"preprint","_id":"7675","doi":"10.1101/2020.04.08.029405","date_published":"2020-04-09T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8155"}]},"date_created":"2020-04-23T10:12:51Z","day":"09","publication":"bioRxiv","language":[{"iso":"eng"}],"publication_status":"published","year":"2020","month":"04","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2020.04.08.029405 ","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology."}]},{"day":"10","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:7460","date_published":"2020-02-10T00:00:00Z","date_created":"2020-02-06T14:56:53Z","page":"155","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria."},"title":"The hole system of triangulated shapes","author":[{"id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","orcid":"0000-0002-4672-8297","full_name":"Ölsböck, Katharina","last_name":"Ölsböck"}],"article_processing_charge":"No","file":[{"creator":"koelsboe","date_updated":"2020-07-14T12:47:58Z","file_size":76195184,"date_created":"2020-02-06T14:43:54Z","file_name":"thesis_ist-final_noack.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","file_id":"7461"},{"file_name":"latex-files.zip","date_created":"2020-02-06T14:52:45Z","file_size":122103715,"date_updated":"2020-07-14T12:47:58Z","creator":"koelsboe","checksum":"7a52383c812b0be64d3826546509e5a4","file_id":"7462","description":"latex source files, figures","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"6608","status":"public","relation":"part_of_dissertation"}]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","abstract":[{"text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.","lang":"eng"}],"month":"02","alternative_title":["ISTA Thesis"],"ddc":["514"],"supervisor":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:15:30Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:58Z","_id":"7460","status":"public","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"}},{"related_material":{"record":[{"id":"6677","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"creator":"dernst","file_size":1622742,"date_updated":"2020-07-14T12:48:04Z","file_name":"2020_Thesis_Kamath.pdf","date_created":"2020-05-26T14:08:13Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7897","checksum":"b39e2e1c376f5819b823fb7077491c64"},{"file_id":"7898","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","date_created":"2020-05-26T14:08:23Z","file_name":"Thesis_Kamath.zip","date_updated":"2020-07-14T12:48:04Z","file_size":15301529,"creator":"dernst"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"KrPi"}],"supervisor":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"date_updated":"2023-09-07T13:15:55Z","ddc":["000"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7896","page":"126","doi":"10.15479/AT:ISTA:7896","date_published":"2020-05-25T00:00:00Z","date_created":"2020-05-26T14:08:55Z","has_accepted_license":"1","year":"2020","day":"25","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"}],"article_processing_charge":"No","title":"On the average-case hardness of total search problems","citation":{"chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}]},{"title":"Localizing grouped instances for efficient detection in low-resource scenarios","author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","last_name":"Royer","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"external_id":{"arxiv":["2004.12623"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093288.","ista":"Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.","mla":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” IEEE Winter Conference on Applications of Computer Vision, 1716–1725, IEEE, 2020, doi:10.1109/WACV45572.2020.9093288.","apa":"Royer, A., & Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093288","ama":"Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093288","short":"A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","ieee":"A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020."},"article_number":"1716-1725","doi":"10.1109/WACV45572.2020.9093288","date_published":"2020-03-01T00:00:00Z","date_created":"2020-06-07T22:00:53Z","day":"01","publication":"IEEE Winter Conference on Applications of Computer Vision","year":"2020","publisher":"IEEE","quality_controlled":"1","oa":1,"department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:17Z","status":"public","type":"conference","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","start_date":"2020-03-01","location":" Snowmass Village, CO, United States","end_date":"2020-03-05"},"_id":"7936","related_material":{"record":[{"status":"deleted","id":"8331","relation":"dissertation_contains"},{"id":"8390","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781728165530"]},"publication_status":"published","month":"03","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/2004.12623","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures."}]},{"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781728165530"]},"publication_status":"published","related_material":{"record":[{"id":"8331","status":"deleted","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"8390","status":"public"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning."}],"month":"03","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/2008.11995","open_access":"1"}],"date_updated":"2023-09-07T13:16:17Z","department":[{"_id":"ChLa"}],"_id":"7937","status":"public","type":"conference","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","start_date":"2020-03-01","end_date":"2020-03-05","location":"Snowmass Village, CO, United States"},"day":"01","publication":"2020 IEEE Winter Conference on Applications of Computer Vision","year":"2020","doi":"10.1109/WACV45572.2020.9093635","date_published":"2020-03-01T00:00:00Z","date_created":"2020-06-07T22:00:53Z","quality_controlled":"1","publisher":"IEEE","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093635","apa":"Royer, A., & Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In 2020 IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093635","short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","ieee":"A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in 2020 IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” 2020 IEEE Winter Conference on Applications of Computer Vision, 2180–2189, IEEE, 2020, doi:10.1109/WACV45572.2020.9093635.","ista":"Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189.","chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093635."},"title":"A flexible selection scheme for minimum-effort transfer learning","author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"article_processing_charge":"No","external_id":{"arxiv":["2008.11995"]},"article_number":"2180-2189"},{"oa_version":"None","abstract":[{"lang":"eng","text":"Multiple-environment Markov decision processes (MEMDPs) are MDPs equipped with not one, but multiple probabilistic transition functions, which represent the various possible unknown environments. While the previous research on MEMDPs focused on theoretical properties for long-run average payoff, we study them with discounted-sum payoff and focus on their practical advantages and applications. MEMDPs can be viewed as a special case of Partially observable and Mixed observability MDPs: the state of the system is perfectly observable, but not the environment. We show that the specific structure of MEMDPs allows for more efficient algorithmic analysis, in particular for faster belief updates. We demonstrate the applicability of MEMDPs in several domains. In particular, we formalize the sequential decision-making approach to contextual recommendation systems as MEMDPs and substantially improve over the previous MDP approach."}],"intvolume":" 30","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["23340835"],"eissn":["23340843"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8390"}]},"volume":30,"_id":"8193","status":"public","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","location":"Nancy, France","end_date":"2020-10-30","start_date":"2020-10-26"},"type":"conference","date_updated":"2023-09-07T13:16:18Z","department":[{"_id":"KrCh"}],"acknowledgement":"Krishnendu Chatterjee is supported by the Austrian ScienceFund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE),and COST Action GAMENET. Petr Novotn ́y is supported bythe Czech Science Foundation grant No. GJ19-15134Y.","quality_controlled":"1","publisher":"Association for the Advancement of Artificial Intelligence","publication":"Proceedings of the 30th International Conference on Automated Planning and Scheduling","day":"01","year":"2020","date_created":"2020-08-02T22:00:58Z","date_published":"2020-06-01T00:00:00Z","page":"48-56","project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” Proceedings of the 30th International Conference on Automated Planning and Scheduling, vol. 30, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","short":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, A. Royer, in:, Proceedings of the 30th International Conference on Automated Planning and Scheduling, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","ieee":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, and A. Royer, “Multiple-environment Markov decision processes: Efficient analysis and applications,” in Proceedings of the 30th International Conference on Automated Planning and Scheduling, Nancy, France, 2020, vol. 30, pp. 48–56.","apa":"Chatterjee, K., Chmelik, M., Karkhanis, D., Novotný, P., & Royer, A. (2020). Multiple-environment Markov decision processes: Efficient analysis and applications. In Proceedings of the 30th International Conference on Automated Planning and Scheduling (Vol. 30, pp. 48–56). Nancy, France: Association for the Advancement of Artificial Intelligence.","ama":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. Multiple-environment Markov decision processes: Efficient analysis and applications. In: Proceedings of the 30th International Conference on Automated Planning and Scheduling. Vol 30. Association for the Advancement of Artificial Intelligence; 2020:48-56.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Deep Karkhanis, Petr Novotný, and Amélie Royer. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” In Proceedings of the 30th International Conference on Automated Planning and Scheduling, 30:48–56. Association for the Advancement of Artificial Intelligence, 2020.","ista":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. 2020. Multiple-environment Markov decision processes: Efficient analysis and applications. Proceedings of the 30th International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 30, 48–56."},"title":"Multiple-environment Markov decision processes: Efficient analysis and applications","article_processing_charge":"No","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"first_name":"Deep","full_name":"Karkhanis, Deep","last_name":"Karkhanis"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný","full_name":"Novotný, Petr"},{"first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","last_name":"Royer"}]},{"date_updated":"2023-09-07T13:16:18Z","department":[{"_id":"ChLa"}],"_id":"8092","status":"public","type":"book_chapter","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030306717"]},"related_material":{"record":[{"id":"8331","status":"deleted","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"8390"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html."}],"month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1711.05139","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Royer A, Bousmalis K, Gouws S, Bertsch F, Mosseri I, Cole F, Murphy K. 2020.XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Domain Adaptation for Visual Understanding. , 33–49.","chicago":"Royer, Amélie, Konstantinos Bousmalis, Stephan Gouws, Fred Bertsch, Inbar Mosseri, Forrester Cole, and Kevin Murphy. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” In Domain Adaptation for Visual Understanding, edited by Richa Singh, Mayank Vatsa, Vishal M. Patel, and Nalini Ratha, 33–49. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-30671-7_3.","apa":"Royer, A., Bousmalis, K., Gouws, S., Bertsch, F., Mosseri, I., Cole, F., & Murphy, K. (2020). XGAN: Unsupervised image-to-image translation for many-to-many mappings. In R. Singh, M. Vatsa, V. M. Patel, & N. Ratha (Eds.), Domain Adaptation for Visual Understanding (pp. 33–49). Springer Nature. https://doi.org/10.1007/978-3-030-30671-7_3","ama":"Royer A, Bousmalis K, Gouws S, et al. XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Singh R, Vatsa M, Patel VM, Ratha N, eds. Domain Adaptation for Visual Understanding. Springer Nature; 2020:33-49. doi:10.1007/978-3-030-30671-7_3","ieee":"A. Royer et al., “XGAN: Unsupervised image-to-image translation for many-to-many mappings,” in Domain Adaptation for Visual Understanding, R. Singh, M. Vatsa, V. M. Patel, and N. Ratha, Eds. Springer Nature, 2020, pp. 33–49.","short":"A. Royer, K. Bousmalis, S. Gouws, F. Bertsch, I. Mosseri, F. Cole, K. Murphy, in:, R. Singh, M. Vatsa, V.M. Patel, N. Ratha (Eds.), Domain Adaptation for Visual Understanding, Springer Nature, 2020, pp. 33–49.","mla":"Royer, Amélie, et al. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” Domain Adaptation for Visual Understanding, edited by Richa Singh et al., Springer Nature, 2020, pp. 33–49, doi:10.1007/978-3-030-30671-7_3."},"editor":[{"first_name":"Richa","full_name":"Singh, Richa","last_name":"Singh"},{"last_name":"Vatsa","full_name":"Vatsa, Mayank","first_name":"Mayank"},{"last_name":"Patel","full_name":"Patel, Vishal M.","first_name":"Vishal M."},{"last_name":"Ratha","full_name":"Ratha, Nalini","first_name":"Nalini"}],"title":"XGAN: Unsupervised image-to-image translation for many-to-many mappings","article_processing_charge":"No","external_id":{"arxiv":["1711.05139"]},"author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie"},{"first_name":"Konstantinos","full_name":"Bousmalis, Konstantinos","last_name":"Bousmalis"},{"first_name":"Stephan","last_name":"Gouws","full_name":"Gouws, Stephan"},{"first_name":"Fred","full_name":"Bertsch, Fred","last_name":"Bertsch"},{"last_name":"Mosseri","full_name":"Mosseri, Inbar","first_name":"Inbar"},{"full_name":"Cole, Forrester","last_name":"Cole","first_name":"Forrester"},{"full_name":"Murphy, Kevin","last_name":"Murphy","first_name":"Kevin"}],"publication":"Domain Adaptation for Visual Understanding","day":"08","year":"2020","date_created":"2020-07-05T22:00:46Z","date_published":"2020-01-08T00:00:00Z","doi":"10.1007/978-3-030-30671-7_3","page":"33-49","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2020-06-08T00:49:46Z","date_published":"2020-06-09T00:00:00Z","doi":"10.15479/AT:ISTA:7944","page":"160","day":"09","year":"2020","has_accepted_license":"1","title":"Reconfiguration problems","article_processing_charge":"No","author":[{"first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana","last_name":"Masárová"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944"},"month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","id":"7950","status":"public"},{"relation":"part_of_dissertation","id":"5986","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"creator":"zmasarov","date_updated":"2020-07-14T12:48:05Z","file_size":13661779,"date_created":"2020-06-08T00:34:00Z","file_name":"THESIS_Zuzka_Masarova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"df688bc5a82b50baee0b99d25fc7b7f0","file_id":"7945"},{"file_id":"7946","checksum":"45341a35b8f5529c74010b7af43ac188","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","date_created":"2020-06-08T00:35:30Z","creator":"zmasarov","file_size":32184006,"date_updated":"2020-07-14T12:48:05Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-005-3"]},"keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"status":"public","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"dissertation","_id":"7944","file_date_updated":"2020-07-14T12:48:05Z","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"ddc":["516","514"],"date_updated":"2023-09-07T13:17:37Z","supervisor":[{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}]},{"article_number":"164302","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"A path-integral approach to composite impurities","grant_number":"M02641"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/1.5144759.","ista":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302.","mla":"Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:10.1063/1.5144759.","ama":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 2020;152(16). doi:10.1063/1.5144759","apa":"Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., & Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5144759","ieee":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” The Journal of Chemical Physics, vol. 152, no. 16. AIP Publishing, 2020.","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020)."},"title":"Intermolecular forces and correlations mediated by a phonon bath","article_processing_charge":"No","external_id":{"isi":["000530448300001"],"arxiv":["1912.02658"]},"author":[{"first_name":"Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Xiang"},{"last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868.","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","publication":"The Journal of Chemical Physics","day":"27","year":"2020","isi":1,"date_created":"2020-09-30T10:33:17Z","doi":"10.1063/1.5144759","date_published":"2020-04-27T00:00:00Z","_id":"8587","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-07T13:16:42Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"intvolume":" 152","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"ec_funded":1,"volume":152,"related_material":{"record":[{"id":"8958","status":"public","relation":"dissertation_contains"}]},"issue":"16"},{"acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","publisher":"Institute of Science and Technology Austria","oa":1,"day":"08","has_accepted_license":"1","year":"2020","date_published":"2020-09-08T00:00:00Z","doi":"10.15479/AT:ISTA:8341","date_created":"2020-09-08T08:53:53Z","page":"215","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341."},"title":"In vitro reconstitution of a Rab activation switch","author":[{"full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level."}],"month":"09","alternative_title":["ISTA Thesis"],"file":[{"creator":"dernst","date_updated":"2021-09-16T12:49:12Z","file_size":65246782,"date_created":"2020-09-08T09:00:29Z","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"70871b335a595252a66c6bbf0824fb02","file_id":"8342"},{"date_updated":"2021-09-16T12:49:12Z","file_size":31259058,"creator":"dernst","date_created":"2020-09-08T09:00:27Z","file_name":"2020_Urban_Bezeljak_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"59a62275088b00b7241e6ff4136434c7","file_id":"8343"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"id":"7580","status":"public","relation":"part_of_dissertation"}]},"_id":"8341","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"ddc":["570"],"supervisor":[{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"date_updated":"2023-09-07T13:17:06Z","file_date_updated":"2021-09-16T12:49:12Z","department":[{"_id":"MaLo"}]},{"title":"Stochastic activation and bistability in a Rab GTPase regulatory network","author":[{"first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","last_name":"Bezeljak"},{"first_name":"Hrushikesh","full_name":"Loya, Hrushikesh","last_name":"Loya"},{"last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saunders","full_name":"Saunders, Timothy E.","first_name":"Timothy E."},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"article_processing_charge":"No","external_id":{"isi":["000521821800040"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:10.1073/pnas.1921027117.","apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” Proceedings of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020.","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549."},"project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"doi":"10.1073/pnas.1921027117","date_published":"2020-03-24T00:00:00Z","date_created":"2020-03-12T05:32:26Z","page":"6504-6549","day":"24","publication":"Proceedings of the National Academy of Sciences","isi":1,"year":"2020","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"department":[{"_id":"MaLo"},{"_id":"CaBe"}],"date_updated":"2023-09-07T13:17:06Z","status":"public","article_type":"original","type":"journal_article","_id":"7580","volume":117,"issue":"12","related_material":{"link":[{"url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"8341","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","month":"03","intvolume":" 117","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"author":[{"id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf","full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057","last_name":"Huszár"}],"article_processing_charge":"No","title":"Combinatorial width parameters for 3-dimensional manifolds","citation":{"apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032","ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"xviii+120","doi":"10.15479/AT:ISTA:8032","date_published":"2020-06-26T00:00:00Z","date_created":"2020-06-26T10:00:36Z","has_accepted_license":"1","year":"2020","day":"26","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2020-07-14T12:48:08Z","department":[{"_id":"UlWa"}],"supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"},{"first_name":"Jonathan","full_name":"Spreer, Jonathan","last_name":"Spreer"}],"date_updated":"2023-09-07T13:18:27Z","ddc":["514"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8032","related_material":{"record":[{"id":"6556","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"7093"}]},"publication_identifier":{"isbn":["978-3-99078-006-0"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3","file_id":"8034","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Kristof_Huszar-Thesis.pdf","date_created":"2020-06-26T10:03:58Z","file_size":2637562,"date_updated":"2020-07-14T12:48:08Z","creator":"khuszar"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"8035","checksum":"d5f8456202b32f4a77552ef47a2837d1","file_size":7163491,"date_updated":"2020-07-14T12:48:08Z","creator":"khuszar","file_name":"Kristof_Huszar-Thesis-source.zip","date_created":"2020-06-26T10:10:06Z"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"06","acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"abstract":[{"text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.","lang":"eng"}],"oa_version":"Published Version"},{"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In Computer Aided Verification, 12224:275–98. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53288-8_14.","ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” Computer Aided Verification, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:10.1007/978-3-030-53288-8_14.","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: Computer Aided Verification. Vol 12224. Springer Nature; 2020:275-298. doi:10.1007/978-3-030-53288-8_14","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2020). Refinement for structured concurrent programs. In Computer Aided Verification (Vol. 12224, pp. 275–298). Springer Nature. https://doi.org/10.1007/978-3-030-53288-8_14","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in Computer Aided Verification, 2020, vol. 12224, pp. 275–298."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000695276000014"]},"author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"}],"title":"Refinement for structured concurrent programs","acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2020","has_accepted_license":"1","isi":1,"publication":"Computer Aided Verification","day":"14","page":"275-298","date_created":"2020-08-03T11:45:35Z","date_published":"2020-07-14T00:00:00Z","doi":"10.1007/978-3-030-53288-8_14","_id":"8195","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","date_updated":"2023-09-07T13:18:00Z","ddc":["000"],"file_date_updated":"2020-08-06T08:14:54Z","department":[{"_id":"ToHe"}],"abstract":[{"text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 12224","month":"07","publication_status":"published","publication_identifier":{"eisbn":["9783030532888"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030532871"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":804237,"date_updated":"2020-08-06T08:14:54Z","file_name":"2020_LNCS_Kragl.pdf","date_created":"2020-08-06T08:14:54Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8201"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8332","status":"public"}]},"volume":12224},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"publication_status":"published","publication_identifier":{"isbn":["9781450376136"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1145/3385412.3385980","open_access":"1"}],"scopus_import":"1","month":"06","abstract":[{"lang":"eng","text":"Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos."}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T13:18:00Z","conference":{"start_date":"2020-06-15","location":"London, United Kingdom","end_date":"2020-06-20","name":"PLDI: Programming Language Design and Implementation"},"type":"conference","status":"public","_id":"8012","page":"227-242","date_created":"2020-06-25T11:40:16Z","doi":"10.1145/3385412.3385980","date_published":"2020-06-01T00:00:00Z","year":"2020","isi":1,"publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","day":"01","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","article_processing_charge":"No","external_id":{"isi":["000614622300016"]},"author":[{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"},{"full_name":"Enea, Constantin","last_name":"Enea","first_name":"Constantin"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Suha Orhun","full_name":"Mutluergil, Suha Orhun","last_name":"Mutluergil"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"}],"title":"Inductive sequentialization of asynchronous programs","citation":{"chicago":"Kragl, Bernhard, Constantin Enea, Thomas A Henzinger, Suha Orhun Mutluergil, and Shaz Qadeer. “Inductive Sequentialization of Asynchronous Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 227–42. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385980.","ista":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. 2020. Inductive sequentialization of asynchronous programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 227–242.","mla":"Kragl, Bernhard, et al. “Inductive Sequentialization of Asynchronous Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–42, doi:10.1145/3385412.3385980.","ama":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. Inductive sequentialization of asynchronous programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:227-242. doi:10.1145/3385412.3385980","apa":"Kragl, B., Enea, C., Henzinger, T. A., Mutluergil, S. O., & Qadeer, S. (2020). Inductive sequentialization of asynchronous programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 227–242). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385980","ieee":"B. Kragl, C. Enea, T. A. Henzinger, S. O. Mutluergil, and S. Qadeer, “Inductive sequentialization of asynchronous programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 227–242.","short":"B. Kragl, C. Enea, T.A. Henzinger, S.O. Mutluergil, S. Qadeer, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–242."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas"}],"article_processing_charge":"No","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","citation":{"ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"135","date_published":"2020-09-10T00:00:00Z","doi":"10.15479/AT:ISTA:8358","date_created":"2020-09-10T09:26:49Z","has_accepted_license":"1","year":"2020","day":"10","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","file_date_updated":"2020-09-11T07:48:10Z","department":[{"_id":"MaLo"}],"supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"date_updated":"2023-09-07T13:18:51Z","ddc":["572"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8358","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7572"},{"relation":"part_of_dissertation","status":"public","id":"7197"}]},"publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"pcaldas","date_updated":"2020-09-10T12:11:29Z","file_size":141602462,"date_created":"2020-09-10T12:11:29Z","file_name":"phd_thesis_pcaldas.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8364","checksum":"882f93fe9c351962120e2669b84bf088","success":1},{"access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_id":"8365","creator":"pcaldas","date_updated":"2020-09-11T07:48:10Z","file_size":450437458,"date_created":"2020-09-10T12:18:17Z","file_name":"phd_thesis_latex_pcaldas.zip"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version"},{"status":"public","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"conference":{"end_date":"2020-09-09","location":"Virtual, Online; Pisa, Italy","start_date":"2020-09-07","name":"ESA: Annual European Symposium on Algorithms"},"type":"conference","_id":"8703","file_date_updated":"2020-10-27T14:31:52Z","department":[{"_id":"HeEd"}],"ddc":["000"],"date_updated":"2023-09-07T13:29:00Z","intvolume":" 173","month":"08","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Even though Delaunay originally introduced his famous triangulations in the case of infinite point sets with translational periodicity, a software that computes such triangulations in the general case is not yet available, to the best of our knowledge. Combining and generalizing previous work, we present a practical algorithm for computing such triangulations. The algorithm has been implemented and experiments show that its performance is as good as the one of the CGAL package, which is restricted to cubic periodicity. "}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","related_material":{"record":[{"id":"9056","status":"public","relation":"dissertation_contains"}]},"volume":173,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"fe0f7c49a99ed870c671b911e10d5496","file_id":"8712","file_size":733291,"date_updated":"2020-10-27T14:31:52Z","creator":"cziletti","file_name":"2020_LIPIcs_Osang.pdf","date_created":"2020-10-27T14:31:52Z"}],"publication_status":"published","publication_identifier":{"issn":["18688969"],"isbn":["9783959771627"]},"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"article_number":"75","title":"Generalizing CGAL periodic Delaunay triangulations","article_processing_charge":"No","author":[{"last_name":"Osang","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rouxel-Labbé","full_name":"Rouxel-Labbé, Mael","first_name":"Mael"},{"full_name":"Teillaud, Monique","last_name":"Teillaud","first_name":"Monique"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Osang, Georg F, Mael Rouxel-Labbé, and Monique Teillaud. “Generalizing CGAL Periodic Delaunay Triangulations.” In 28th Annual European Symposium on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ESA.2020.75.","ista":"Osang GF, Rouxel-Labbé M, Teillaud M. 2020. Generalizing CGAL periodic Delaunay triangulations. 28th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 75.","mla":"Osang, Georg F., et al. “Generalizing CGAL Periodic Delaunay Triangulations.” 28th Annual European Symposium on Algorithms, vol. 173, 75, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.75.","ama":"Osang GF, Rouxel-Labbé M, Teillaud M. Generalizing CGAL periodic Delaunay triangulations. In: 28th Annual European Symposium on Algorithms. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.75","apa":"Osang, G. F., Rouxel-Labbé, M., & Teillaud, M. (2020). Generalizing CGAL periodic Delaunay triangulations. In 28th Annual European Symposium on Algorithms (Vol. 173). Virtual, Online; Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.75","short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"G. F. Osang, M. Rouxel-Labbé, and M. Teillaud, “Generalizing CGAL periodic Delaunay triangulations,” in 28th Annual European Symposium on Algorithms, Virtual, Online; Pisa, Italy, 2020, vol. 173."},"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2020-10-25T23:01:18Z","date_published":"2020-08-26T00:00:00Z","doi":"10.4230/LIPIcs.ESA.2020.75","publication":"28th Annual European Symposium on Algorithms","day":"26","year":"2020","has_accepted_license":"1"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"9418","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html"}]},"date_published":"2020-04-26T00:00:00Z","date_created":"2020-02-11T09:07:37Z","has_accepted_license":"1","publication_status":"published","year":"2020","day":"26","file":[{"file_id":"7482","checksum":"8d372ea5defd8cb8fdc430111ed754a9","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-02-11T09:07:27Z","file_name":"main.pdf","creator":"bphuong","date_updated":"2020-07-14T12:47:59Z","file_size":405469}],"publication":"8th International Conference on Learning Representations","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"month":"04","abstract":[{"text":"We address the following question: How redundant is the parameterisation of ReLU networks? Specifically, we consider transformations of the weight space which leave the function implemented by the network intact. Two such transformations are known for feed-forward architectures: permutation of neurons within a layer, and positive scaling of all incoming weights of a neuron coupled with inverse scaling of its outgoing weights. In this work, we show for architectures with non-increasing widths that permutation and scaling are in fact the only function-preserving weight transformations. For any eligible architecture we give an explicit construction of a neural network such that any other network that implements the same function can be obtained from the original one by the application of permutations and rescaling. The proof relies on a geometric understanding of boundaries between linear regions of ReLU networks, and we hope the developed mathematical tools are of independent interest.","lang":"eng"}],"oa_version":"Published Version","author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:59Z","title":"Functional vs. parametric equivalence of ReLU networks","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:29:50Z","citation":{"ista":"Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020.","apa":"Phuong, M., & Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In 8th International Conference on Learning Representations. Online.","ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: 8th International Conference on Learning Representations. ; 2020.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"type":"conference","conference":{"end_date":"2020-04-30","location":"Online","start_date":"2020-04-27","name":"ICLR: International Conference on Learning Representations"},"status":"public","_id":"7481"},{"main_file_link":[{"url":"https://arxiv.org/abs/1904.08647","open_access":"1"}],"scopus_import":"1","intvolume":" 52","month":"02","abstract":[{"text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum.","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"}]},"volume":52,"issue":"1","publication_status":"published","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"language":[{"iso":"eng"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"status":"public","_id":"9781","department":[{"_id":"RoSe"}],"date_updated":"2023-09-07T13:30:11Z","ddc":["510"],"oa":1,"quality_controlled":"1","publisher":"Society for Industrial & Applied Mathematics ","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","page":"605-622","date_created":"2021-08-06T07:34:16Z","doi":"10.1137/19m126284x","date_published":"2020-02-12T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"SIAM Journal on Mathematical Analysis","day":"12","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]},"author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","citation":{"mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis, vol. 52, no. 1, Society for Industrial & Applied Mathematics , 2020, pp. 605–22, doi:10.1137/19m126284x.","apa":"Feliciangeli, D., & Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics . https://doi.org/10.1137/19m126284x","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 2020;52(1):605-622. doi:10.1137/19m126284x","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” SIAM Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial & Applied Mathematics , pp. 605–622, 2020.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics , 2020. https://doi.org/10.1137/19m126284x.","ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"ddc":["530","532"],"date_updated":"2023-09-07T13:30:45Z","file_date_updated":"2020-11-20T09:14:22Z","department":[{"_id":"JuFi"}],"_id":"7489","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"dernst","date_updated":"2020-11-20T09:14:22Z","file_size":1897571,"date_created":"2020-11-20T09:14:22Z","file_name":"2020_ArchRatMechAn_Fischer.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f107e21b58f5930876f47144be37cf6c","file_id":"8779","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00039527"],"eissn":["14320673"]},"publication_status":"published","volume":236,"related_material":{"record":[{"status":"public","id":"10007","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy.","lang":"eng"}],"month":"05","intvolume":" 236","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:10.1007/s00205-019-01486-2.","ieee":"J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” Archive for Rational Mechanics and Analysis, vol. 236. Springer Nature, pp. 967–1087, 2020.","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","apa":"Fischer, J. L., & Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01486-2","ama":"Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 2020;236:967-1087. doi:10.1007/s00205-019-01486-2","chicago":"Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-019-01486-2.","ista":"Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087."},"title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel"}],"external_id":{"isi":["000511060200001"]},"article_processing_charge":"Yes (via OA deal)","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"day":"01","publication":"Archive for Rational Mechanics and Analysis","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-05-01T00:00:00Z","doi":"10.1007/s00205-019-01486-2","date_created":"2020-02-16T23:00:50Z","page":"967-1087","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"related_material":{"record":[{"status":"public","id":"10007","relation":"dissertation_contains"}]},"date_published":"2020-03-11T00:00:00Z","date_created":"2021-09-13T12:17:11Z","ec_funded":1,"day":"11","language":[{"iso":"eng"}],"publication":"arXiv","year":"2020","publication_status":"submitted","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/2003.05478","open_access":"1"}],"oa":1,"oa_version":"Preprint","acknowledgement":"Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385.","abstract":[{"text":"We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a \"gradient flow calibration\" ensures that the route of steepest descent in the energy landscape is unique and stable.","lang":"eng"}],"department":[{"_id":"JuFi"}],"title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","author":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","last_name":"Hensel"},{"first_name":"Tim","full_name":"Laux, Tim","last_name":"Laux"},{"first_name":"Thilo","full_name":"Simon, Thilo","last_name":"Simon"}],"external_id":{"arxiv":["2003.05478"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-09-07T13:30:45Z","citation":{"chicago":"Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, n.d.","ista":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.","mla":"Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, 2003.05478.","short":"J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.).","ieee":"J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” arXiv. .","ama":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.","apa":"Fischer, J. L., Hensel, S., Laux, T., & Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv."},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"status":"public","type":"preprint","article_number":"2003.05478","_id":"10012"},{"acknowledgement":"The authors acknowledge the support from I. Prieto and the IST Nanofabrication Facility. This work was supported by IST Austria and a NOMIS foundation research grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European Union’s Horizon 2020 research and innovation programs under grant agreement No 732894 (FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). ","publisher":"American Physical Society","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"29","publication":"Physical Review Applied","doi":"10.1103/PhysRevApplied.14.044055","date_published":"2020-10-29T00:00:00Z","date_created":"2020-11-15T23:01:17Z","article_number":"044055","project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644"},{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"mla":"Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied, vol. 14, no. 4, 044055, American Physical Society, 2020, doi:10.1103/PhysRevApplied.14.044055.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 2020;14(4). doi:10.1103/PhysRevApplied.14.044055","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.14.044055","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor,” Physical Review Applied, vol. 14, no. 4. American Physical Society, 2020.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020).","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied. American Physical Society, 2020. https://doi.org/10.1103/PhysRevApplied.14.044055.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea","last_name":"Trioni"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"},{"first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"external_id":{"arxiv":["2007.01644"],"isi":["000582797300003"]},"article_processing_charge":"No","title":"Surpassing the resistance quantum with a geometric superinductor","acknowledged_ssus":[{"_id":"NanoFab"}],"abstract":[{"text":"The superconducting circuit community has recently discovered the promising potential of superinductors. These circuit elements have a characteristic impedance exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of ground state charge fluctuations. Applications include the realization of hardware protected qubits for fault tolerant quantum computing, improved coupling to small dipole moment objects and defining a new quantum metrology standard for the ampere. In this work we refute the widespread notion that superinductors can only be implemented based on kinetic inductance, i.e. using disordered superconductors or Josephson junction arrays. We present modeling, fabrication and characterization of 104 planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled tunneling events and offer high reproducibility, linearity and the ability to couple magnetically - properties that significantly broaden the scope of future quantum circuits. ","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 14","publication_identifier":{"eissn":["23317019"]},"publication_status":"published","file":[{"date_created":"2021-03-29T11:43:20Z","file_name":"2020_PhysReviewApplied_Peruzzo.pdf","creator":"dernst","date_updated":"2021-03-29T11:43:20Z","file_size":2607823,"checksum":"2a634abe75251ae7628cd54c8a4ce2e8","file_id":"9300","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"4","volume":14,"related_material":{"record":[{"status":"public","id":"13070","relation":"research_data"},{"relation":"dissertation_contains","id":"9920","status":"public"}]},"ec_funded":1,"_id":"8755","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-07T13:31:22Z","ddc":["530"],"department":[{"_id":"JoFi"}],"file_date_updated":"2021-03-29T11:43:20Z"},{"status":"public","article_type":"original","type":"journal_article","_id":"7573","department":[{"_id":"JaMa"}],"date_updated":"2023-09-07T13:31:05Z","month":"07","intvolume":" 139","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.05757"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport."}],"issue":"7","volume":139,"related_material":{"record":[{"id":"10030","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00217824"]},"publication_status":"published","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Homogenisation of one-dimensional discrete optimal transport","author":[{"full_name":"Gladbach, Peter","last_name":"Gladbach","first_name":"Peter"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Portinale, Lorenzo","last_name":"Portinale","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000539439400008"],"arxiv":["1905.05757"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234.","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees. Elsevier, 2020. https://doi.org/10.1016/j.matpur.2020.02.008.","apa":"Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. Elsevier. https://doi.org/10.1016/j.matpur.2020.02.008","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 2020;139(7):204-234. doi:10.1016/j.matpur.2020.02.008","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7. Elsevier, pp. 204–234, 2020.","mla":"Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:10.1016/j.matpur.2020.02.008."},"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.","doi":"10.1016/j.matpur.2020.02.008","date_published":"2020-07-01T00:00:00Z","date_created":"2020-03-08T23:00:47Z","page":"204-234","day":"01","publication":"Journal de Mathematiques Pures et Appliquees","isi":1,"year":"2020"},{"_id":"10022","article_number":"2008.10962","type":"preprint","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"status":"public","date_updated":"2023-09-07T13:31:05Z","citation":{"chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, n.d.","ista":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962.","mla":"Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962.","ama":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv.","apa":"Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv.","short":"D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” arXiv. ."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","full_name":"Forkert, Dominik L","last_name":"Forkert"},{"last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","last_name":"Portinale","full_name":"Portinale, Lorenzo"}],"article_processing_charge":"No","external_id":{"arxiv":["2008.10962"]},"department":[{"_id":"JaMa"}],"title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","abstract":[{"lang":"eng","text":"We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality."}],"oa_version":"Preprint","acknowledgement":"This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245.","main_file_link":[{"url":"https://arxiv.org/abs/2008.10962","open_access":"1"}],"oa":1,"month":"08","publication_status":"submitted","year":"2020","day":"25","publication":"arXiv","language":[{"iso":"eng"}],"page":"33","date_published":"2020-08-25T00:00:00Z","related_material":{"record":[{"id":"11739","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"10030"}]},"ec_funded":1,"date_created":"2021-09-17T10:57:27Z"},{"year":"2020","has_accepted_license":"1","publication":"Proceedings of the 37th International Conference on Machine Learning","day":"12","page":"5416-5425","date_created":"2020-11-05T15:25:58Z","date_published":"2020-07-12T00:00:00Z","acknowledgement":"Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","oa":1,"quality_controlled":"1","publisher":"ML Research Press","citation":{"ama":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.","apa":"Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425). Online: ML Research Press.","ieee":"N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in Proceedings of the 37th International Conference on Machine Learning, Online, 2020, vol. 119, pp. 5416–5425.","short":"N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425.","mla":"Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 5416–25.","ista":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.","chicago":"Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In Proceedings of the 37th International Conference on Machine Learning, 119:5416–25. ML Research Press, 2020."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2002.10384"]},"author":[{"first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H"},{"first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias","last_name":"Frantar"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"title":"On the sample complexity of adversarial multi-source PAC learning","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"issn":["2640-3498"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-02-15T09:00:01Z","file_name":"2020_PMLR_Konstantinov.pdf","creator":"dernst","date_updated":"2021-02-15T09:00:01Z","file_size":281286,"file_id":"9120","checksum":"cc755d0054bc4b2be778ea7aa7884d2f","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"10799","status":"public"}],"link":[{"url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf","relation":"supplementary_material"}]},"volume":119,"abstract":[{"text":"We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 119","month":"07","date_updated":"2023-09-07T13:42:08Z","ddc":["000"],"file_date_updated":"2021-02-15T09:00:01Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"_id":"8724","conference":{"end_date":"2020-07-18","location":"Online","start_date":"2020-07-12","name":"ICML: International Conference on Machine Learning"},"type":"conference","status":"public"},{"file":[{"file_id":"8650","checksum":"c9238fff422e7a957c3a0d559f756b3a","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-12T12:18:47Z","file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","date_updated":"2020-10-12T12:18:47Z","file_size":2725143,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["13672630"]},"publication_status":"published","related_material":{"record":[{"id":"10759","status":"public","relation":"dissertation_contains"}]},"issue":"9","volume":22,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures."}],"month":"09","intvolume":" 22","scopus_import":"1","ddc":["530"],"date_updated":"2023-09-07T13:44:16Z","file_date_updated":"2020-10-12T12:18:47Z","department":[{"_id":"MiLe"}],"_id":"8644","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","publication":"New Journal of Physics","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-09-01T00:00:00Z","doi":"10.1088/1367-2630/abae44","date_created":"2020-10-11T22:01:14Z","acknowledgement":"We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44","ama":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44","ieee":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020.","short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","mla":"Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44.","ista":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026.","chicago":"Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44."},"title":"Detecting composite orders in layered models via machine learning","author":[{"orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech"},{"first_name":"N","full_name":"Defenu, N","last_name":"Defenu"},{"first_name":"S","full_name":"Chiacchiera, S","last_name":"Chiacchiera"},{"first_name":"A","last_name":"Trombettoni","full_name":"Trombettoni, A"},{"last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000573298000001"]},"article_number":"093026","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","name":"Analytic and machine learning approaches to composite quantum impurities","grant_number":"25681"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02641","name":"A path-integral approach to composite impurities"}]},{"date_updated":"2023-09-07T13:43:51Z","ddc":["530"],"file_date_updated":"2020-10-27T12:49:04Z","department":[{"_id":"RoSe"}],"_id":"8705","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["1424-0637"]},"publication_status":"published","file":[{"file_name":"2020_Annales_Mysliwy.pdf","date_created":"2020-10-27T12:49:04Z","creator":"cziletti","file_size":469831,"date_updated":"2020-10-27T12:49:04Z","success":1,"checksum":"c12c9c1e6f08def245e42f3cb1d83827","file_id":"8711","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"12","volume":21,"related_material":{"record":[{"relation":"dissertation_contains","id":"11473","status":"public"}]},"ec_funded":1,"abstract":[{"text":"We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 21","citation":{"ista":"Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025.","chicago":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare. Springer Nature, 2020. https://doi.org/10.1007/s00023-020-00969-3.","apa":"Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-020-00969-3","ama":"Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025. doi:10.1007/s00023-020-00969-3","ieee":"K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” Annales Henri Poincare, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020.","short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.","mla":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:10.1007/s00023-020-00969-3."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof","last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"external_id":{"isi":["000578111800002"],"arxiv":["2003.12371"]},"article_processing_charge":"Yes (via OA deal)","title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Annales Henri Poincare","page":"4003-4025","doi":"10.1007/s00023-020-00969-3","date_published":"2020-12-01T00:00:00Z","date_created":"2020-10-25T23:01:19Z","acknowledgement":"Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria)","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"quality_controlled":"1","publisher":"Springer Nature","isi":1,"year":"2020","day":"03","publication":"International Journal on Software Tools for Technology Transfer","page":"741-758","date_published":"2020-08-03T00:00:00Z","doi":"10.1007/s10009-020-00582-z","date_created":"2022-03-18T10:10:53Z","citation":{"ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.","chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer. Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758.","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-020-00582-z","mla":"Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"full_name":"Lebeltel, Olivier","last_name":"Lebeltel","first_name":"Olivier"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"},{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Ulus","full_name":"Ulus, Dogan","first_name":"Dogan"}],"article_processing_charge":"No","external_id":{"isi":["000555398600001"]},"title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","abstract":[{"lang":"eng","text":"We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance."}],"oa_version":"None","scopus_import":"1","month":"08","intvolume":" 22","publication_identifier":{"issn":["1433-2779"],"eissn":["1433-2787"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":22,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"299"}]},"_id":"10861","type":"journal_article","article_type":"original","status":"public","keyword":["Information Systems","Software"],"date_updated":"2023-09-08T11:52:02Z","department":[{"_id":"ToHe"}]},{"status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7569","file_date_updated":"2020-07-14T12:48:00Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"ddc":["000","570"],"date_updated":"2023-09-12T11:02:24Z","month":"02","intvolume":" 16","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models."}],"issue":"2","volume":16,"related_material":{"record":[{"id":"9716","status":"deleted","relation":"research_data"},{"id":"9776","status":"public","relation":"research_data"},{"relation":"used_in_publication","id":"9779","status":"public"},{"relation":"dissertation_contains","id":"8155","status":"public"},{"status":"public","id":"9777","relation":"research_data"}]},"file":[{"file_id":"7579","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-03-09T15:12:21Z","file_name":"2020_PlosCompBio_Grah.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:00Z","file_size":2209325}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","article_number":"e1007642","title":"The relation between crosstalk and gene regulation form revisited","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"}],"article_processing_charge":"No","external_id":{"isi":["000526725200019"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.","mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020.","apa":"Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642","ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642"},"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642","date_created":"2020-03-06T07:39:38Z","day":"25","publication":"PLOS Computational Biology","has_accepted_license":"1","isi":1,"year":"2020"},{"author":[{"full_name":"Santini, Laura","last_name":"Santini","first_name":"Laura"},{"last_name":"Halbritter","full_name":"Halbritter, Florian","first_name":"Florian"},{"last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian","first_name":"Fabian"},{"full_name":"Suzuki, Toru","last_name":"Suzuki","first_name":"Toru"},{"last_name":"Asami","full_name":"Asami, Maki","first_name":"Maki"},{"first_name":"Julia","full_name":"Ramesmayer, Julia","last_name":"Ramesmayer"},{"first_name":"Xiaoyan","last_name":"Ma","full_name":"Ma, Xiaoyan"},{"first_name":"Andreas","last_name":"Lackner","full_name":"Lackner, Andreas"},{"last_name":"Warr","full_name":"Warr, Nick","first_name":"Nick"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ernest","full_name":"Laue, Ernest","last_name":"Laue"},{"first_name":"Matthias","last_name":"Farlik","full_name":"Farlik, Matthias"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"full_name":"Perry, Anthony C. F.","last_name":"Perry","first_name":"Anthony C. F."},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"pmid":["PPR234457 "]},"title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","department":[{"_id":"SiHi"}],"date_updated":"2023-09-12T11:05:28Z","citation":{"mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","status":"public","_id":"8813","doi":"10.1101/2020.11.03.366948","date_published":"2020-11-05T00:00:00Z","date_created":"2020-11-26T07:17:19Z","year":"2020","publication_status":"submitted","day":"05","language":[{"iso":"eng"}],"publication":"bioRxiv","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"oa":1,"month":"11","abstract":[{"lang":"eng","text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation."}],"oa_version":"Preprint","pmid":1},{"status":"public","type":"research_data_reference","_id":"9777","title":"Maximizing crosstalk","department":[{"_id":"GaTk"}],"author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"},{"first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-12T11:02:25Z","citation":{"ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002.","chicago":"Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.","apa":"Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002."},"month":"02","publisher":"Public Library of Science","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pcbi.1007642.s002"}],"oa_version":"None","date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642.s002","related_material":{"record":[{"status":"public","id":"7569","relation":"used_in_publication"}]},"date_created":"2021-08-06T07:21:51Z","day":"25","year":"2020"},{"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step."}],"oa_version":"Published Version","related_material":{"record":[{"id":"133","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8012"},{"relation":"part_of_dissertation","id":"8195","status":"public"},{"status":"public","id":"160","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"creator":"bkragl","date_updated":"2020-09-04T12:17:47Z","file_size":1348815,"date_created":"2020-09-04T12:17:47Z","file_name":"kragl-thesis.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"26fe261550f691280bda4c454bf015c7","file_id":"8333"},{"checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"kragl-thesis.zip","date_created":"2020-09-04T13:00:17Z","file_size":372312,"date_updated":"2020-09-04T13:00:17Z","creator":"bkragl"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","_id":"8332","department":[{"_id":"ToHe"}],"file_date_updated":"2020-09-04T13:00:17Z","supervisor":[{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-13T08:45:08Z","ddc":["000"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"120","date_published":"2020-09-03T00:00:00Z","doi":"10.15479/AT:ISTA:8332","date_created":"2020-09-04T12:24:12Z","has_accepted_license":"1","year":"2020","day":"03","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl"}],"article_processing_charge":"No","title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","citation":{"mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"department":[{"_id":"JaMa"}],"date_updated":"2023-09-18T08:13:15Z","type":"journal_article","article_type":"original","status":"public","_id":"71","issue":"3","volume":52,"publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.01092","open_access":"1"}],"month":"10","intvolume":" 52","abstract":[{"text":"We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric.","lang":"eng"}],"oa_version":"Preprint","publist_id":"7983","author":[{"last_name":"Gladbach","full_name":"Gladbach, Peter","first_name":"Peter"},{"full_name":"Kopfer, Eva","last_name":"Kopfer","first_name":"Eva"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"article_processing_charge":"No","external_id":{"isi":["000546975100017"],"arxiv":["1809.01092"]},"title":"Scaling limits of discrete optimal transport","citation":{"mla":"Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440.","ieee":"P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020.","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802.","apa":"Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440","ama":"Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440","chicago":"Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440.","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"2759-2802","date_published":"2020-10-01T00:00:00Z","doi":"10.1137/19M1243440","date_created":"2018-12-11T11:44:28Z","isi":1,"year":"2020","day":"01","publication":"SIAM Journal on Mathematical Analysis","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","oa":1},{"department":[{"_id":"ChWo"}],"file_date_updated":"2020-10-08T08:34:53Z","date_updated":"2023-09-18T09:30:01Z","ddc":["006"],"type":"journal_article","article_type":"original","status":"public","_id":"5681","volume":26,"issue":"6","publication_identifier":{"issn":["10772626"],"eissn":["19410506"]},"publication_status":"published","file":[{"date_created":"2020-10-08T08:34:53Z","file_name":"preprint.pdf","creator":"wojtan","date_updated":"2020-10-08T08:34:53Z","file_size":21910098,"checksum":"8d4c55443a0ee335bb5bb652de503042","file_id":"8626","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 26","abstract":[{"text":"We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"oa_version":"Submitted Version","author":[{"full_name":"Hikaru, Ibayashi","last_name":"Hikaru","first_name":"Ibayashi"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"last_name":"Thuerey","full_name":"Thuerey, Nils","first_name":"Nils"},{"full_name":"Igarashi, Takeo","last_name":"Igarashi","first_name":"Takeo"},{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"}],"article_processing_charge":"No","external_id":{"pmid":["30507534"],"isi":["000532295600014"]},"title":"Simulating liquids on dynamically warping grids","citation":{"ista":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302.","chicago":"Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628.","apa":"Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628","ama":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","ieee":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020.","mla":"Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"2288-2302","date_published":"2020-06-01T00:00:00Z","doi":"10.1109/TVCG.2018.2883628","date_created":"2018-12-16T22:59:21Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"IEEE Transactions on Visualization and Computer Graphics","quality_controlled":"1","publisher":"IEEE","oa":1,"acknowledgement":"This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion."},{"date_created":"2020-12-21T09:44:30Z","doi":"10.15479/AT:ISTA:8958","date_published":"2020-12-21T00:00:00Z","page":"125","day":"21","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"Rotation of coupled cold molecules in the presence of a many-body environment","article_processing_charge":"No","author":[{"first_name":"Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Xiang"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958."},"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5886"},{"status":"public","id":"8587","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1120"}]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"3994c54a1241451d561db1d4f43bad30","file_id":"8967","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"THESIS_Xiang_Li.pdf","date_created":"2020-12-22T10:55:56Z","file_size":3622305,"date_updated":"2020-12-22T10:55:56Z","creator":"xli"},{"access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","file_id":"8968","checksum":"0954ecfc5554c05615c14de803341f00","creator":"xli","date_updated":"2020-12-30T07:18:03Z","file_size":4018859,"date_created":"2020-12-22T10:56:03Z","file_name":"THESIS_Xiang_Li.zip"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"file_date_updated":"2020-12-30T07:18:03Z","department":[{"_id":"MiLe"}],"ddc":["539"],"date_updated":"2023-09-20T11:30:58Z","supervisor":[{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"status":"public","type":"dissertation","_id":"8958"},{"acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2020","day":"14","page":"148","date_published":"2020-09-14T00:00:00Z","doi":"10.15479/AT:ISTA:8386","date_created":"2020-09-14T01:04:53Z","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"642841","name":"Distributed 3D Object Design"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"citation":{"ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","abstract":[{"lang":"eng","text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting."}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"Thesis_Ran.zip","date_created":"2020-09-14T01:02:59Z","creator":"rzhang","file_size":1245800191,"date_updated":"2020-09-14T12:18:43Z","file_id":"8388","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8396","checksum":"817e20c33be9247f906925517c56a40d","creator":"rzhang","file_size":161385316,"date_updated":"2020-09-15T12:51:53Z","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","date_created":"2020-09-15T12:51:53Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"486","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1002"}]},"ec_funded":1,"_id":"8386","type":"dissertation","status":"public","supervisor":[{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-22T09:49:31Z","ddc":["003"],"department":[{"_id":"BeBi"}],"file_date_updated":"2020-09-15T12:51:53Z"},{"department":[{"_id":"GeKa"}],"file_date_updated":"2020-07-14T12:48:07Z","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"date_updated":"2023-09-26T15:50:22Z","ddc":["530"],"type":"dissertation","status":"public","_id":"7996","related_material":{"record":[{"status":"public","id":"1328","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7541"},{"relation":"part_of_dissertation","status":"public","id":"77"},{"relation":"part_of_dissertation","status":"public","id":"23"},{"relation":"part_of_dissertation","id":"840","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"7997","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"closed","file_name":"JK_thesis_latex_source_files.zip","date_created":"2020-06-22T09:22:04Z","file_size":392794743,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1de716bf110dbd77d383e479232bf496","file_id":"7998","file_size":28453247,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst","file_name":"PhD_thesis_JK_pdfa.pdf","date_created":"2020-06-22T09:21:29Z"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Kukucka, Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"}],"article_processing_charge":"No","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","citation":{"chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria.","mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"178","doi":"10.15479/AT:ISTA:7996","date_published":"2020-06-22T00:00:00Z","date_created":"2020-06-22T09:22:23Z","has_accepted_license":"1","year":"2020","day":"22","publisher":"Institute of Science and Technology Austria","oa":1},{"publication_status":"published","publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030532901"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-08-17T11:32:44Z","file_size":625056,"creator":"dernst","date_created":"2020-08-17T11:32:44Z","file_name":"2020_LNCS_CAV_Chatterjee.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8276","checksum":"093d4788d7d5b2ce0ffe64fbe7820043","success":1}],"ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"12738"}]},"volume":12225,"abstract":[{"text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 12225","month":"07","date_updated":"2023-10-03T11:36:13Z","ddc":["000"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-08-17T11:32:44Z","_id":"8272","conference":{"name":"CAV: Computer Aided Verification"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","year":"2020","has_accepted_license":"1","isi":1,"publication":"International Conference on Computer Aided Verification","day":"14","page":"398-420","date_created":"2020-08-16T22:00:58Z","date_published":"2020-07-14T00:00:00Z","doi":"10.1007/978-3-030-53291-8_21","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000695272500021"],"arxiv":["2005.04018"]},"article_processing_charge":"No","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Katoen","full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"first_name":"Maximilian","full_name":"Weininger, Maximilian","last_name":"Weininger"},{"first_name":"Tobias","full_name":"Winkler, Tobias","last_name":"Winkler"}],"title":"Stochastic games with lexicographic reachability-safety objectives","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}]},{"project":[{"call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","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"}],"author":[{"last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"external_id":{"isi":["000611826500008"]},"article_processing_charge":"No","editor":[{"last_name":"Tran","full_name":"Tran, Phong ","first_name":"Phong "}],"title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","citation":{"chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61. Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006.","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier. https://doi.org/10.1016/bs.mcb.2020.01.006","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"145-161","doi":"10.1016/bs.mcb.2020.01.006","date_published":"2020-02-27T00:00:00Z","date_created":"2020-03-08T23:00:47Z","isi":1,"year":"2020","day":"27","publication":"Methods in Cell Biology","type":"book_chapter","status":"public","_id":"7572","department":[{"_id":"MaLo"}],"date_updated":"2023-10-04T09:50:24Z","alternative_title":["Methods in Cell Biology"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"month":"02","intvolume":" 158","abstract":[{"lang":"eng","text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material."}],"oa_version":"Preprint","related_material":{"record":[{"id":"8358","status":"public","relation":"part_of_dissertation"}]},"volume":158,"ec_funded":1,"publication_identifier":{"issn":["0091679X"]},"publication_status":"published","language":[{"iso":"eng"}]},{"article_processing_charge":"No","external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"author":[{"orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S."},{"last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Víctor M.","full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora"},{"last_name":"Alfonso","full_name":"Alfonso, Carlos","first_name":"Carlos"},{"id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"first_name":"Germán","last_name":"Rivas","full_name":"Rivas, Germán"},{"first_name":"Waldemar","full_name":"Vollmer, Waldemar","last_name":"Vollmer"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","citation":{"ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5.","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","ieee":"N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"}],"page":"407-417","date_created":"2020-01-28T16:14:41Z","doi":"10.1038/s41564-019-0657-5","date_published":"2020-01-20T00:00:00Z","year":"2020","isi":1,"publication":"Nature Microbiology","day":"20","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","department":[{"_id":"MaLo"}],"date_updated":"2023-10-06T12:22:38Z","type":"journal_article","article_type":"letter_note","status":"public","_id":"7387","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","status":"public","id":"14280"}]},"volume":5,"publication_status":"published","publication_identifier":{"issn":["2058-5276"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"scopus_import":"1","intvolume":" 5","month":"01","abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}],"pmid":1,"oa_version":"Submitted Version"},{"date_created":"2020-07-24T07:09:18Z","date_published":"2020-07-24T00:00:00Z","doi":"10.1556/012.2020.57.2.1454","page":"193-199","publication":"Studia Scientiarum Mathematicarum Hungarica","day":"24","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Akadémiai Kiadó","acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","article_processing_charge":"No","external_id":{"isi":["000570978400005"]},"author":[{"last_name":"Vegter","full_name":"Vegter, Gert","first_name":"Gert"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.","apa":"Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454.","ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454."},"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize"}],"ec_funded":1,"volume":57,"issue":"2","language":[{"iso":"eng"}],"file":[{"date_created":"2020-07-24T07:09:06Z","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","date_updated":"2020-07-24T07:09:06Z","file_size":1476072,"creator":"mwintrae","file_id":"8164","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["0081-6906"],"eissn":["1588-2896"]},"intvolume":" 57","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.","lang":"eng"}],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-24T07:09:06Z","ddc":["510"],"date_updated":"2023-10-10T13:05:27Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","_id":"8163"},{"project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"author":[{"first_name":"A.","last_name":"Shakiba","full_name":"Shakiba, A."},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Hooshmandasl","full_name":"Hooshmandasl, M.R.","first_name":"M.R."},{"last_name":"Alambardar Meybodi","full_name":"Alambardar Meybodi, M.","first_name":"M."}],"article_processing_charge":"No","external_id":{"arxiv":["1805.10672"]},"title":"A note on belief structures and s-approximation spaces","citation":{"mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117.","apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.","chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.","ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Iranian Academic Center for Education, Culture and Research","quality_controlled":"1","oa":1,"acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","page":"117-128","date_published":"2020-10-01T00:00:00Z","doi":"10.29252/ijmsi.15.2.117","date_created":"2020-10-18T22:01:36Z","has_accepted_license":"1","year":"2020","day":"01","publication":"Iranian Journal of Mathematical Sciences and Informatics","type":"journal_article","article_type":"original","status":"public","_id":"8671","file_date_updated":"2020-10-19T11:14:20Z","department":[{"_id":"KrCh"}],"date_updated":"2023-10-16T09:25:00Z","ddc":["000"],"scopus_import":"1","month":"10","intvolume":" 15","abstract":[{"lang":"eng","text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. "}],"oa_version":"Submitted Version","volume":15,"issue":"2","publication_identifier":{"eissn":["2008-9473"],"issn":["1735-4463"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f299661a6d51cda6d255a76be696f48d","file_id":"8676","success":1,"creator":"dernst","date_updated":"2020-10-19T11:14:20Z","file_size":261688,"date_created":"2020-10-19T11:14:20Z","file_name":"2020_ijmsi_Shakiba_accepted.pdf"}],"language":[{"iso":"eng"}]},{"scopus_import":"1","month":"07","intvolume":" 25","abstract":[{"text":"The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.","lang":"eng"}],"oa_version":"Published Version","volume":25,"publication_identifier":{"eissn":["1083-6489"]},"publication_status":"published","file":[{"success":1,"file_id":"8549","checksum":"8e7c42e72596f6889d786e8e8b89994f","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_EJournProbab_Dareiotis.pdf","date_created":"2020-09-21T13:15:02Z","file_size":273042,"date_updated":"2020-09-21T13:15:02Z","creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6359","file_date_updated":"2020-09-21T13:15:02Z","department":[{"_id":"JaMa"}],"date_updated":"2023-10-16T09:22:50Z","ddc":["510"],"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"doi":"10.1214/20-EJP479","date_published":"2020-07-16T00:00:00Z","date_created":"2019-04-30T07:40:17Z","isi":1,"has_accepted_license":"1","year":"2020","day":"16","publication":"Electronic Journal of Probability","article_number":"82","author":[{"first_name":"Konstantinos","full_name":"Dareiotis, Konstantinos","last_name":"Dareiotis"},{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","full_name":"Gerencser, Mate","last_name":"Gerencser"}],"article_processing_charge":"No","external_id":{"arxiv":["1812.04583"],"isi":["000550150700001"]},"title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","citation":{"ama":"Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP479","apa":"Dareiotis, K., & Gerencser, M. (2020). On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP479","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).","ieee":"K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","mla":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP479.","ista":"Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 25, 82.","chicago":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP479."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":30224591,"date_updated":"2020-09-14T13:39:14Z","file_name":"2020_Thesis_Royer.pdf","date_created":"2020-09-14T13:39:14Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8391","checksum":"c914d2f88846032f3d8507734861b6ee"},{"relation":"main_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"8392","checksum":"ae98fb35d912cff84a89035ae5794d3c","creator":"dernst","file_size":74227627,"date_updated":"2020-09-14T13:39:17Z","file_name":"thesis_sources.zip","date_created":"2020-09-14T13:39:17Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7936","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7937"},{"id":"8193","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8092"},{"status":"public","id":"911","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","date_updated":"2023-10-16T10:04:02Z","supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"department":[{"_id":"ChLa"}],"file_date_updated":"2020-09-14T13:39:17Z","_id":"8390","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","year":"2020","has_accepted_license":"1","day":"14","page":"197","date_created":"2020-09-14T13:42:09Z","date_published":"2020-09-14T00:00:00Z","doi":"10.15479/AT:ISTA:8390","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer","first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87"}],"title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models"},{"year":"2020","has_accepted_license":"1","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","day":"01","page":"7498-7507","date_created":"2020-07-31T16:53:49Z","doi":"10.1109/CVPR42600.2020.00752","date_published":"2020-07-01T00:00:00Z","oa":1,"publisher":"IEEE","quality_controlled":"1","citation":{"ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752","apa":"Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752.","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2004.04180"]},"author":[{"first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445","last_name":"Henderson"},{"first_name":"Vagia","full_name":"Tsiminaki, Vagia","last_name":"Tsiminaki"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"title":"Leveraging 2D data to learn textured 3D mesh generation","publication_status":"published","publication_identifier":{"eisbn":["9781728171685"],"eissn":["2575-7075"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8187","success":1,"date_updated":"2020-07-31T16:57:12Z","file_size":10262773,"creator":"phenders","date_created":"2020-07-31T16:57:12Z","file_name":"paper.pdf"}],"abstract":[{"lang":"eng","text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf","open_access":"1"}],"scopus_import":"1","month":"07","date_updated":"2023-10-17T07:37:11Z","ddc":["004"],"department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-31T16:57:12Z","_id":"8186","conference":{"end_date":"2020-06-19","location":"Virtual","start_date":"2020-06-14","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"type":"conference","status":"public"},{"intvolume":" 15","month":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements.","lang":"eng"}],"volume":15,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"status":"public","article_type":"original","type":"journal_article","_id":"7416","department":[{"_id":"JiFr"}],"date_updated":"2023-10-17T09:01:48Z","oa":1,"publisher":"Taylor & Francis","quality_controlled":"1","date_created":"2020-01-30T10:12:04Z","date_published":"2020-01-01T00:00:00Z","doi":"10.1080/15592324.2019.1687175","publication":"Plant Signaling & Behavior","day":"01","year":"2020","isi":1,"article_number":"1687175","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","article_processing_charge":"No","external_id":{"pmid":["31696764"],"isi":["000494909300001"]},"author":[{"last_name":"Sinclair","orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"last_name":"Krämer","full_name":"Krämer, U.","first_name":"U."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior, vol. 15, no. 1, 1687175, Taylor & Francis, 2020, doi:10.1080/15592324.2019.1687175.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687175","apa":"Sinclair, S. A., & Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2019.1687175","short":"S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020).","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” Plant Signaling & Behavior, vol. 15, no. 1. Taylor & Francis, 2020.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior. Taylor & Francis, 2020. https://doi.org/10.1080/15592324.2019.1687175.","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 15(1), 1687175."}},{"article_processing_charge":"No","external_id":{"arxiv":["1709.05202"],"isi":["000558100500002"]},"author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072"},{"first_name":"Tommaso","full_name":"Rosati, Tommaso","last_name":"Rosati"}],"title":"Modelled distributions of Triebel–Lizorkin type","citation":{"ista":"Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297.","chicago":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica. Instytut Matematyczny, 2020. https://doi.org/10.4064/sm180411-11-2.","ama":"Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 2020;252(3):251-297. doi:10.4064/sm180411-11-2","apa":"Hensel, S., & Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. Instytut Matematyczny. https://doi.org/10.4064/sm180411-11-2","short":"S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297.","ieee":"S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” Studia Mathematica, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020.","mla":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:10.4064/sm180411-11-2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"251-297","date_created":"2021-02-25T08:55:03Z","date_published":"2020-03-01T00:00:00Z","doi":"10.4064/sm180411-11-2","year":"2020","isi":1,"publication":"Studia Mathematica","day":"01","quality_controlled":"1","publisher":"Instytut Matematyczny","department":[{"_id":"JuFi"},{"_id":"GradSch"}],"date_updated":"2023-10-17T09:15:53Z","type":"journal_article","article_type":"original","keyword":["General Mathematics"],"status":"public","_id":"9196","volume":252,"issue":"3","publication_status":"published","publication_identifier":{"eissn":["1730-6337"],"issn":["0039-3223"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 252","month":"03","abstract":[{"text":"In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \\textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces.","lang":"eng"}],"oa_version":"Preprint"},{"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 16","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":4551246,"date_updated":"2020-07-14T12:47:59Z","file_name":"2020_PLOSPatho_Dick.pdf","date_created":"2020-02-11T10:07:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"a297f54d1fef0efe4789ca00f37f241e","file_id":"7484"}],"publication_status":"published","publication_identifier":{"issn":["1553-7374"]},"issue":"1","volume":16,"related_material":{"record":[{"relation":"research_data","id":"9723","status":"deleted"}]},"_id":"7464","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-10-17T12:29:34Z","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"FlSc"}],"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","publication":"PLOS Pathogens","day":"27","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-02-06T18:47:17Z","doi":"10.1371/journal.ppat.1008277","date_published":"2020-01-27T00:00:00Z","article_number":"e1008277","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020)."},"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","external_id":{"isi":["000510746400010"],"pmid":["31986188"]},"article_processing_charge":"No","author":[{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"first_name":"Dustin R.","full_name":"Morado, Dustin R.","last_name":"Morado"},{"full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"last_name":"Lyddon","full_name":"Lyddon, Terri D.","first_name":"Terri D."},{"first_name":"Arianna M.","full_name":"Broad, Arianna M.","last_name":"Broad"},{"first_name":"J. Ryan","last_name":"Feathers","full_name":"Feathers, J. Ryan"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"first_name":"Juan R.","full_name":"Perilla, Juan R.","last_name":"Perilla"},{"first_name":"John A. G.","last_name":"Briggs","full_name":"Briggs, John A. G."},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}]},{"project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"}],"article_number":"e1007494","author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"external_id":{"arxiv":["1906.02785"],"isi":["000510916500025"]},"article_processing_charge":"No","title":"Limits on amplifiers of natural selection under death-Birth updating","citation":{"mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020.","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"date_published":"2020-01-17T00:00:00Z","doi":"10.1371/journal.pcbi.1007494","date_created":"2019-12-23T13:45:11Z","isi":1,"has_accepted_license":"1","year":"2020","day":"17","publication":"PLoS computational biology","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7212","file_date_updated":"2020-07-14T12:47:53Z","department":[{"_id":"KrCh"}],"date_updated":"2023-10-17T12:29:47Z","ddc":["000"],"scopus_import":"1","month":"01","intvolume":" 16","abstract":[{"lang":"eng","text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"7196","status":"public"}]},"volume":16,"ec_funded":1,"publication_identifier":{"eissn":["15537358"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ce32ee2d2f53aed832f78bbd47e882df","file_id":"7441","date_updated":"2020-07-14T12:47:53Z","file_size":1817531,"creator":"dernst","date_created":"2020-02-03T07:32:42Z","file_name":"2020_PlosCompBio_Tkadlec.pdf"}],"language":[{"iso":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196."},"title":"A role of graphs in evolutionary processes","author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"}],"article_processing_charge":"No","day":"12","has_accepted_license":"1","year":"2020","date_published":"2020-01-12T00:00:00Z","doi":"10.15479/AT:ISTA:7196","date_created":"2019-12-20T12:26:36Z","page":"144","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["519"],"supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"date_updated":"2023-10-17T12:29:46Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:52Z","_id":"7196","status":"public","type":"dissertation","file":[{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","file_id":"7255","date_updated":"2020-07-14T12:47:52Z","file_size":21100497,"creator":"jtkadlec","date_created":"2020-01-12T11:49:49Z","file_name":"thesis.zip"},{"date_created":"2020-01-28T07:32:42Z","file_name":"2020_Tkadlec_Thesis.pdf","date_updated":"2020-07-14T12:47:52Z","file_size":11670983,"creator":"dernst","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","file_id":"7367","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"7210","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"5751","status":"public"},{"relation":"dissertation_contains","status":"public","id":"7212"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time."}],"month":"01","alternative_title":["ISTA Thesis"]},{"citation":{"short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","mla":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","chicago":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1912.10095"]},"author":[{"full_name":"Shevchenko, Alexander","last_name":"Shevchenko","first_name":"Alexander"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"}],"title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"year":"2020","has_accepted_license":"1","publication":"Proceedings of the 37th International Conference on Machine Learning","day":"13","page":"8773-8784","date_created":"2021-02-25T09:36:22Z","date_published":"2020-07-13T00:00:00Z","acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","oa":1,"quality_controlled":"1","publisher":"ML Research Press","date_updated":"2023-10-17T12:43:19Z","ddc":["000"],"file_date_updated":"2021-03-02T15:38:14Z","department":[{"_id":"MaMo"}],"_id":"9198","type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"2020_PMLR_Shevchenko.pdf","date_created":"2021-03-02T15:38:14Z","file_size":5336380,"date_updated":"2021-03-02T15:38:14Z","creator":"dernst","success":1,"file_id":"9217","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":119,"abstract":[{"lang":"eng","text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks."}],"oa_version":"Published Version","intvolume":" 119","month":"07"},{"abstract":[{"text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy.","lang":"eng"}],"oa_version":"Published Version","month":"06","intvolume":" 8","publication_identifier":{"issn":["2544-7297"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9171","checksum":"cea41de9937d07a3b927d71ee8b4e432","success":1,"date_updated":"2021-02-19T13:56:24Z","file_size":562359,"creator":"dernst","date_created":"2021-02-19T13:56:24Z","file_name":"2020_CompMathBiophysics_Akopyan2.pdf"}],"language":[{"iso":"eng"}],"volume":8,"issue":"1","ec_funded":1,"_id":"9157","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-10-17T12:34:51Z","ddc":["510"],"department":[{"_id":"HeEd"}],"file_date_updated":"2021-02-19T13:56:24Z","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","publisher":"De Gruyter","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2020","day":"20","publication":"Computational and Mathematical Biophysics","page":"51-67","doi":"10.1515/cmb-2020-0100","date_published":"2020-06-20T00:00:00Z","date_created":"2021-02-17T15:13:01Z","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"article_processing_charge":"No","title":"The weighted mean curvature derivative of a space-filling diagram"},{"ddc":["510"],"date_updated":"2023-10-17T12:35:10Z","file_date_updated":"2021-02-19T13:33:19Z","department":[{"_id":"HeEd"}],"_id":"9156","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2021-02-19T13:33:19Z","file_name":"2020_CompMathBiophysics_Akopyan.pdf","creator":"dernst","date_updated":"2021-02-19T13:33:19Z","file_size":707452,"checksum":"ca43a7440834eab6bbea29c59b56ef3a","file_id":"9170","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["2544-7297"]},"ec_funded":1,"issue":"1","volume":8,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy."}],"intvolume":" 8","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88."},"title":"The weighted Gaussian curvature derivative of a space-filling diagram","external_id":{"arxiv":["1908.06777"]},"article_processing_charge":"No","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"publication":"Computational and Mathematical Biophysics","day":"21","year":"2020","has_accepted_license":"1","date_created":"2021-02-17T15:12:44Z","doi":"10.1515/cmb-2020-0101","date_published":"2020-07-21T00:00:00Z","page":"74-88","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","oa":1,"publisher":"De Gruyter","quality_controlled":"1"},{"year":"2020","has_accepted_license":"1","isi":1,"publication":"Electronic Journal of Probability","day":"21","date_created":"2020-12-27T23:01:17Z","doi":"10.1214/20-EJP536","date_published":"2020-10-21T00:00:00Z","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","oa":1,"quality_controlled":"1","publisher":" Institute of Mathematical Statistics","citation":{"mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536.","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"author":[{"full_name":"Redig, Frank","last_name":"Redig","first_name":"Frank"},{"first_name":"Ellen","full_name":"Saada, Ellen","last_name":"Saada"},{"id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico","last_name":"Sau","full_name":"Sau, Federico"}],"title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","article_number":"138","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","publication_identifier":{"eissn":["1083-6489"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8976","checksum":"d75359b9814e78d57c0a481b7cde3751","success":1,"creator":"dernst","date_updated":"2020-12-28T08:24:08Z","file_size":696653,"date_created":"2020-12-28T08:24:08Z","file_name":"2020_ElectronJProbab_Redig.pdf"}],"ec_funded":1,"volume":25,"abstract":[{"text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 25","month":"10","date_updated":"2023-10-17T12:51:56Z","ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-12-28T08:24:08Z","_id":"8973","type":"journal_article","article_type":"original","status":"public"},{"publication_identifier":{"issn":["0012-7094"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":169,"issue":"16","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1805.10715","open_access":"1"}],"month":"09","intvolume":" 169","date_updated":"2023-10-17T12:51:10Z","department":[{"_id":"TiBr"}],"_id":"179","article_type":"original","type":"journal_article","status":"public","isi":1,"year":"2020","day":"10","publication":"Duke Mathematical Journal","page":"3099-3165","date_published":"2020-09-10T00:00:00Z","doi":"10.1215/00127094-2020-0031","date_created":"2018-12-11T11:45:02Z","publisher":"Duke University Press","quality_controlled":"1","oa":1,"citation":{"ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. 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Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"pmid":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"scopus_import":"1","intvolume":" 125","month":"07","publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"language":[{"iso":"eng"}],"volume":125,"issue":"4","article_number":"043202","citation":{"ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 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Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000552227400008"],"pmid":["32794788"],"arxiv":["1912.10218"]},"author":[{"last_name":"Malia","full_name":"Malia, Benjamin K.","first_name":"Benjamin K."},{"first_name":"Julián","full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón"},{"last_name":"Wu","full_name":"Wu, Yunfan","first_name":"Yunfan"},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"},{"first_name":"Mark A.","last_name":"Kasevich","full_name":"Kasevich, Mark A."}],"title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2020","isi":1,"publication":"Physical Review Letters","day":"24","date_created":"2020-08-24T06:24:04Z","doi":"10.1103/PhysRevLett.125.043202","date_published":"2020-07-24T00:00:00Z"},{"publication_status":"published","year":"2020","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"language":[{"iso":"eng"}],"publication":"OSA Quantum 2.0 Conference","day":"01","date_created":"2021-11-21T23:01:31Z","doi":"10.1364/QUANTUM.2020.QTu8A.1","date_published":"2020-01-01T00:00:00Z","abstract":[{"text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient.","lang":"eng"}],"oa_version":"None","publisher":"Optica Publishing Group","scopus_import":"1","quality_controlled":"1","alternative_title":["OSA Technical Digest"],"month":"01","date_updated":"2023-10-18T08:32:34Z","citation":{"ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1.","chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In OSA Quantum 2.0 Conference. Optica Publishing Group, 2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1.","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in OSA Quantum 2.0 Conference, Washington, DC, United States, 2020.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: OSA Quantum 2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States: Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1","mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1, Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Nicholas J.","last_name":"Lambert","full_name":"Lambert, Nicholas J."},{"first_name":"Sonia","full_name":"Mobassem, Sonia","last_name":"Mobassem"},{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez"},{"last_name":"Schwefel","full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L."}],"department":[{"_id":"JoFi"}],"title":"New designs and noise channels in electro-optic microwave to optical up-conversion","_id":"10328","article_number":"QTu8A.1","conference":{"name":"OSA: Optical Society of America","start_date":"2020-09-14","location":"Washington, DC, United States","end_date":"2020-09-17"},"type":"conference","status":"public"},{"title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","article_processing_charge":"No","author":[{"full_name":"Confavreux, Basile J","last_name":"Confavreux","first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"},{"first_name":"Everton J.","full_name":"Agnes, Everton J.","last_name":"Agnes"},{"full_name":"Lillicrap, Timothy","last_name":"Lillicrap","first_name":"Timothy"},{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408.","ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada."},"project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."},{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"date_created":"2021-07-04T22:01:27Z","date_published":"2020-12-06T00:00:00Z","page":"16398-16408","publication":"Advances in Neural Information Processing Systems","day":"06","year":"2020","oa":1,"quality_controlled":"1","acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","department":[{"_id":"TiVo"}],"date_updated":"2023-10-18T09:20:55Z","status":"public","conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2020-12-12","location":"Vancouver, Canada","start_date":"2020-12-06"},"type":"conference","_id":"9633","ec_funded":1,"volume":33,"related_material":{"record":[{"status":"public","id":"14422","relation":"dissertation_contains"}],"link":[{"url":"https://doi.org/10.1101/2020.10.24.353409","relation":"is_continued_by"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1049-5258"]},"intvolume":" 33","month":"12","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}]},{"article_number":"108463","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship","grant_number":"723-2015"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","ieee":"S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” Cell Reports, vol. 33, no. 9. Elsevier, 2020.","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.108463","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463."},"title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","external_id":{"isi":["000595658100018"],"pmid":["33264621"]},"article_processing_charge":"Yes","author":[{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"first_name":"Martin","full_name":"Di Donato, Martin","last_name":"Di Donato"},{"last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"first_name":"Petr","full_name":"Klíma, Petr","last_name":"Klíma"},{"first_name":"Jie","last_name":"Liu","full_name":"Liu, Jie"},{"full_name":"Bailly, Aurélien","last_name":"Bailly","first_name":"Aurélien"},{"first_name":"Noel","last_name":"Ferro","full_name":"Ferro, Noel"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Cell Reports","day":"01","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-12-13T23:01:21Z","doi":"10.1016/j.celrep.2020.108463","date_published":"2020-12-01T00:00:00Z","_id":"8943","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2023-11-16T13:03:31Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-12-14T07:33:39Z","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"intvolume":" 33","month":"12","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2020_CellReports_Tan.pdf","date_created":"2020-12-14T07:33:39Z","file_size":8056434,"date_updated":"2020-12-14T07:33:39Z","creator":"dernst","success":1,"checksum":"ed18cba0fb48ed2e789381a54cc21904","file_id":"8948","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["22111247"]},"ec_funded":1,"issue":"9","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/plants-on-aspirin/"}]},"volume":33},{"issue":"21","volume":117,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"id":"14530","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/","description":"News on IST Homepage"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"publication_status":"published","month":"05","intvolume":" 117","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2005.11190","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"department":[{"_id":"BjHo"}],"date_updated":"2023-11-30T10:55:13Z","status":"public","article_type":"original","type":"journal_article","_id":"7932","date_published":"2020-05-26T00:00:00Z","doi":"10.1073/pnas.1913716117","date_created":"2020-06-07T22:00:51Z","page":"11233-11239","day":"26","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"year":"2020","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","author":[{"full_name":"Xu, Duo","last_name":"Xu","first_name":"Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul"},{"first_name":"Xingyu","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0179-9737","full_name":"Ma, Xingyu","last_name":"Ma"},{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"article_processing_charge":"No","external_id":{"arxiv":["2005.11190"],"isi":["000536797100014"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239.","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","ieee":"D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1913716117","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:10.1073/pnas.1913716117."},"project":[{"name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","grant_number":"I04188","call_identifier":"FWF","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}]},{"file_date_updated":"2023-12-18T10:42:32Z","department":[{"_id":"LaEr"}],"date_updated":"2023-12-18T10:46:09Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["General Mathematics"],"status":"public","_id":"14694","related_material":{"record":[{"id":"6183","status":"public","relation":"earlier_version"}]},"volume":25,"publication_status":"published","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-12-18T10:42:32Z","file_size":1374708,"creator":"dernst","date_created":"2023-12-18T10:42:32Z","file_name":"2020_DocumentaMathematica_Alt.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14695","checksum":"12aacc1d63b852ff9a51c1f6b218d4a6","success":1}],"intvolume":" 25","month":"09","abstract":[{"lang":"eng","text":"We study the unique solution m of the Dyson equation \\( -m(z)^{-1} = z\\1 - a + S[m(z)] \\) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases."}],"oa_version":"Published Version","external_id":{"arxiv":["1804.07752"]},"article_processing_charge":"Yes","author":[{"first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes","last_name":"Alt"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"}],"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","citation":{"mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020, pp. 1421–539, doi:10.4171/dm/780.","short":"J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press, pp. 1421–1539, 2020.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS Press. https://doi.org/10.4171/dm/780","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica. EMS Press, 2020. https://doi.org/10.4171/dm/780.","ista":"Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. 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Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. 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Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, (2020).","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"}],"article_processing_charge":"No","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","file_date_updated":"2020-07-14T12:48:09Z","department":[{"_id":"GaTk"}],"_id":"8097","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"has_accepted_license":"1","year":"2020","file":[{"date_updated":"2020-07-14T12:48:09Z","file_size":255770756,"creator":"bkavcic","date_created":"2020-07-06T20:38:27Z","file_name":"natComm_2020_scripts.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","file_id":"8098"}],"day":"15","doi":"10.15479/AT:ISTA:8097","date_published":"2020-07-15T00:00:00Z","date_created":"2020-07-06T20:40:19Z","contributor":[{"contributor_type":"research_group","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"contributor_type":"research_group","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach"}],"abstract":[{"lang":"eng","text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology."}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"07"}]