[{"month":"01","intvolume":" 40","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation."}],"volume":40,"issue":"1","ec_funded":1,"file":[{"success":1,"file_id":"8150","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_JournNeuroscience_Lombardi.pdf","date_created":"2020-07-22T11:44:48Z","creator":"dernst","file_size":6646046,"date_updated":"2020-07-22T11:44:48Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"8084","file_date_updated":"2020-07-22T11:44:48Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2023-09-05T14:02:55Z","quality_controlled":"1","publisher":"Society for Neuroscience","oa":1,"doi":"10.1523/jneurosci.1278-19.2019","date_published":"2020-01-02T00:00:00Z","date_created":"2020-07-05T15:24:51Z","page":"171-190","day":"02","publication":"Journal of Neuroscience","isi":1,"has_accepted_license":"1","year":"2020","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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","author":[{"full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Manuel","last_name":"Gómez-Extremera","full_name":"Gómez-Extremera, Manuel"},{"last_name":"Bernaola-Galván","full_name":"Bernaola-Galván, Pedro","first_name":"Pedro"},{"first_name":"Ramalingam","last_name":"Vetrivelan","full_name":"Vetrivelan, Ramalingam"},{"full_name":"Saper, Clifford B.","last_name":"Saper","first_name":"Clifford B."},{"first_name":"Thomas E.","last_name":"Scammell","full_name":"Scammell, Thomas E."},{"last_name":"Ivanov","full_name":"Ivanov, Plamen Ch.","first_name":"Plamen Ch."}],"external_id":{"isi":["000505167600016"],"pmid":["31694962"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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."}},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","page":"1217-1271","date_published":"2020-03-09T00:00:00Z","doi":"10.1007/s00205-020-01489-4","date_created":"2020-04-08T15:18:03Z","isi":1,"has_accepted_license":"1","year":"2020","day":"09","publication":"Archive for Rational Mechanics and Analysis","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"author":[{"first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","last_name":"Deuchert"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000519415000001"],"arxiv":["1901.11363"]},"title":"Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature","citation":{"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.","ista":"Deuchert A, Seiringer R. 2020. Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature. Archive for Rational Mechanics and Analysis. 236(6), 1217–1271.","mla":"Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis, vol. 236, no. 6, Springer Nature, 2020, pp. 1217–71, doi:10.1007/s00205-020-01489-4.","short":"A. Deuchert, R. Seiringer, Archive for Rational Mechanics and Analysis 236 (2020) 1217–1271.","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.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"03","intvolume":" 236","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","issue":"6","volume":236,"ec_funded":1,"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"publication_status":"published","file":[{"checksum":"b645fb64bfe95bbc05b3eea374109a9c","file_id":"8785","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-11-20T13:17:42Z","file_name":"2020_ArchRatMechanicsAnalysis_Deuchert.pdf","date_updated":"2020-11-20T13:17:42Z","file_size":704633,"creator":"dernst"}],"language":[{"iso":"eng"}],"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)"},"status":"public","_id":"7650","file_date_updated":"2020-11-20T13:17:42Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-05T14:18:49Z","ddc":["510"]},{"scopus_import":"1","intvolume":" 238","month":"11","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":238,"issue":"11","publication_status":"published","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8826","checksum":"cc67a79a67bef441625fcb1cd031db3d","creator":"dernst","file_size":942343,"date_updated":"2020-12-02T08:50:38Z","file_name":"2020_ArchiveRatMech_Bossmann.pdf","date_created":"2020-12-02T08:50:38Z"}],"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","_id":"8130","department":[{"_id":"RoSe"}],"file_date_updated":"2020-12-02T08:50:38Z","date_updated":"2023-09-05T14:19:06Z","ddc":["510"],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","page":"541-606","date_created":"2020-07-18T15:06:35Z","doi":"10.1007/s00205-020-01548-w","date_published":"2020-11-01T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Archive for Rational Mechanics and Analysis","day":"01","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"external_id":{"arxiv":["1907.04547"],"isi":["000550164400001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","last_name":"Bossmann","full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343"}],"title":"Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons","citation":{"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.","ista":"Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606.","mla":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” Archive for Rational Mechanics and Analysis, vol. 238, no. 11, Springer Nature, 2020, pp. 541–606, doi:10.1007/s00205-020-01548-w.","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","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.","short":"L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"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":"7235","file_date_updated":"2020-11-19T11:13:55Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-05T14:57:29Z","ddc":["510","530"],"scopus_import":"1","month":"09","intvolume":" 180","abstract":[{"lang":"eng","text":"We consider the Fröhlich model of a polaron, and show that its effective mass diverges in thestrong coupling limit."}],"oa_version":"Published Version","volume":180,"ec_funded":1,"publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"publication_status":"published","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"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"last_name":"Lieb","full_name":"Lieb, Elliott H.","first_name":"Elliott H."},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000556199700003"]},"article_processing_charge":"Yes (via OA deal)","title":"Divergence of the effective mass of a polaron in the strong coupling limit","citation":{"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.","ama":"Lieb EH, Seiringer R. Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. 2020;180:23-33. doi:10.1007/s10955-019-02322-3","apa":"Lieb, E. H., & Seiringer, R. (2020). Divergence of the effective mass of a polaron in the strong coupling limit. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-019-02322-3","chicago":"Lieb, Elliott H., and Robert Seiringer. “Divergence of the Effective Mass of a Polaron in the Strong Coupling Limit.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-019-02322-3.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","page":"23-33","date_published":"2020-09-01T00:00:00Z","doi":"10.1007/s10955-019-02322-3","date_created":"2020-01-07T09:42:03Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Journal of Statistical Physics"},{"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt","last_name":"Auerbach","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt"},{"first_name":"Federico","last_name":"Giacon","full_name":"Giacon, Federico"},{"last_name":"Kiltz","full_name":"Kiltz, Eike","first_name":"Eike"}],"external_id":{"isi":["000828688000016"]},"article_processing_charge":"No","title":"Everybody’s a target: Scalability in public-key encryption","citation":{"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.","mla":"Auerbach, Benedikt, et al. “Everybody’s a Target: Scalability in Public-Key Encryption.” Advances in Cryptology – EUROCRYPT 2020, vol. 12107, Springer Nature, 2020, pp. 475–506, doi:10.1007/978-3-030-45727-3_16.","short":"B. Auerbach, F. Giacon, E. Kiltz, in:, Advances in Cryptology – EUROCRYPT 2020, Springer Nature, 2020, pp. 475–506.","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.","ama":"Auerbach B, Giacon F, Kiltz E. Everybody’s a target: Scalability in public-key encryption. In: Advances in Cryptology – EUROCRYPT 2020. Vol 12107. Springer Nature; 2020:475-506. doi:10.1007/978-3-030-45727-3_16","apa":"Auerbach, B., Giacon, F., & Kiltz, E. (2020). Everybody’s a target: Scalability in public-key encryption. In Advances in Cryptology – EUROCRYPT 2020 (Vol. 12107, pp. 475–506). Springer Nature. https://doi.org/10.1007/978-3-030-45727-3_16"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","quality_controlled":"1","oa":1,"page":"475-506","doi":"10.1007/978-3-030-45727-3_16","date_published":"2020-05-01T00:00:00Z","date_created":"2020-06-15T07:13:37Z","isi":1,"year":"2020","day":"01","publication":"Advances in Cryptology – EUROCRYPT 2020","type":"conference","conference":{"end_date":"2020-05-15","start_date":"2020-05-11","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"status":"public","_id":"7966","department":[{"_id":"KrPi"}],"date_updated":"2023-09-05T15:06:40Z","alternative_title":["LNCS"],"main_file_link":[{"url":"https://eprint.iacr.org/2019/364","open_access":"1"}],"month":"05","intvolume":" 12107","abstract":[{"lang":"eng","text":"For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).\r\n\r\nFor Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.\r\n\r\nAs our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem."}],"oa_version":"Submitted Version","volume":12107,"ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030457266","9783030457273"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"Monitorability under assumptions","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"external_id":{"isi":["000728160600001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020, pp. 3–18.","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.","ama":"Henzinger TA, Sarac NE. Monitorability under assumptions. In: Runtime Verification. Vol 12399. Springer Nature; 2020:3-18. doi:10.1007/978-3-030-60508-7_1","apa":"Henzinger, T. A., & Sarac, N. E. (2020). Monitorability under assumptions. In Runtime Verification (Vol. 12399, pp. 3–18). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-60508-7_1","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.","ista":"Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.","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."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","doi":"10.1007/978-3-030-60508-7_1","date_published":"2020-10-02T00:00:00Z","date_created":"2020-10-07T15:05:37Z","page":"3-18","day":"02","publication":"Runtime Verification","has_accepted_license":"1","isi":1,"year":"2020","status":"public","type":"conference","conference":{"start_date":"2020-10-06","end_date":"2020-10-09","location":"Los Angeles, CA, United States","name":"RV: Runtime Verification"},"_id":"8623","department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-15T14:28:06Z","ddc":["000"],"date_updated":"2023-09-05T15:08:26Z","month":"10","intvolume":" 12399","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Submitted Version","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."}],"volume":12399,"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"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030605070","9783030605087"],"issn":["0302-9743"]},"publication_status":"published"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030604394","9783030604400"],"issn":["0302-9743"]},"ec_funded":1,"volume":12301,"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"}],"intvolume":" 12301","month":"10","alternative_title":["LNCS"],"scopus_import":"1","date_updated":"2023-09-05T15:09:16Z","department":[{"_id":"UlWa"}],"_id":"8732","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","publication":"Graph-Theoretic Concepts in Computer Science","day":"09","year":"2020","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","publisher":"Springer Nature","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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.","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.","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."},"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","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara"},{"first_name":"Fabian","last_name":"Klute","full_name":"Klute, Fabian"},{"full_name":"Parada, Irene","last_name":"Parada","first_name":"Irene"},{"full_name":"Seidel, Raimund","last_name":"Seidel","first_name":"Raimund"},{"last_name":"Vogtenhuber","full_name":"Vogtenhuber, Birgit","first_name":"Birgit"},{"last_name":"Wiedera","full_name":"Wiedera, Tilo","first_name":"Tilo"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"title":"Witness maps and applications","editor":[{"first_name":"A","full_name":"Kiayias, A","last_name":"Kiayias"}],"author":[{"last_name":"Chakraborty","full_name":"Chakraborty, Suvradip","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"first_name":"Manoj","last_name":"Prabhakaran","full_name":"Prabhakaran, Manoj"},{"first_name":"Daniel","last_name":"Wichs","full_name":"Wichs, Daniel"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","short":"S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key Cryptography, Springer Nature, Cham, 2020, pp. 220–246.","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.","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.","ista":"Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications. In: Public-Key Cryptography. vol. 12110, 220–246."},"date_published":"2020-04-29T00:00:00Z","doi":"10.1007/978-3-030-45374-9_8","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.","date_updated":"2023-09-05T15:10:02Z","status":"public","type":"book_chapter","_id":"10865","series_title":"LNCS","volume":12110,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030453732","9783030453749"],"issn":["0302-9743"]},"publication_status":"published","month":"04","place":"Cham","intvolume":" 12110","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/090"}],"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) ."}]},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","date_published":"2020-03-12T00:00:00Z","doi":"10.1007/s11005-020-01286-w","date_created":"2020-03-23T11:11:47Z","page":"2143-2174","day":"12","publication":"Letters in Mathematical Physics","isi":1,"has_accepted_license":"1","year":"2020","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"title":"Central limit theorem for Bose gases interacting through singular potentials","author":[{"last_name":"Rademacher","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"}],"external_id":{"isi":["000551556000006"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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."},"month":"03","intvolume":" 110","scopus_import":"1","oa_version":"Published Version","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"}],"volume":110,"ec_funded":1,"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,"file_id":"8784","checksum":"3bdd41f10ad947b67a45b98f507a7d4a"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"publication_status":"published","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":"7611","file_date_updated":"2020-11-20T12:04:26Z","department":[{"_id":"RoSe"}],"ddc":["510"],"date_updated":"2023-09-05T15:14:50Z"},{"intvolume":" 90","month":"02","scopus_import":"1","oa_version":"Published Version","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"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"volume":90,"issue":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2020-02-10T08:18:14Z","file_name":"2020_EcologMono_Baskett.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:54Z","file_size":537941,"file_id":"7469","checksum":"ab8130c6e68101f5a091d05324c36f08","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1557-7015"],"issn":["0012-9615"]},"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)"},"type":"journal_article","article_type":"original","_id":"7236","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:54Z","ddc":["570"],"date_updated":"2023-09-05T15:43:19Z","oa":1,"publisher":"Wiley","quality_controlled":"1","date_created":"2020-01-07T12:47:07Z","doi":"10.1002/ecm.1397","date_published":"2020-02-01T00:00:00Z","publication":"Ecological Monographs","day":"01","year":"2020","has_accepted_license":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e01397","title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000508511600001"]},"author":[{"last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina"},{"full_name":"Schroeder, Lucy","last_name":"Schroeder","first_name":"Lucy"},{"full_name":"Weber, Marjorie G.","last_name":"Weber","first_name":"Marjorie G."},{"last_name":"Schemske","full_name":"Schemske, Douglas W.","first_name":"Douglas W."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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.","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020).","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."}},{"month":"09","intvolume":" 227","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"issue":"5","volume":227,"ec_funded":1,"file":[{"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","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8799","checksum":"8e8150dbbba8cb65b72f81d1f0864b8b","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"publication_status":"published","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":"7697","file_date_updated":"2020-11-24T12:19:38Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-09-05T15:46:04Z","quality_controlled":"1","publisher":"Wiley","oa":1,"date_published":"2020-09-01T00:00:00Z","doi":"10.1111/nph.16629","date_created":"2020-04-30T08:43:29Z","page":"1406-1416","day":"01","publication":"New Phytologist","has_accepted_license":"1","isi":1,"year":"2020","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters","author":[{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hartinger, Corinna","orcid":"0000-0003-1618-2737","last_name":"Hartinger","first_name":"Corinna","id":"AEFB2266-8ABF-11EA-AA39-812C3623CBE4"},{"full_name":"Wang, Xiaojuan","last_name":"Wang","first_name":"Xiaojuan"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"external_id":{"pmid":["32350870"],"isi":["000534092400001"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416.","ama":"Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 2020;227(5):1406-1416. doi:10.1111/nph.16629","apa":"Zhang, Y., Hartinger, C., Wang, X., & Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. Wiley. https://doi.org/10.1111/nph.16629","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.","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."}},{"day":"01","publication":"Computer Graphics Forum","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1111/cgf.13914","date_published":"2020-05-01T00:00:00Z","date_created":"2020-11-17T09:35:10Z","page":"89-99","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.","quality_controlled":"1","publisher":"Wiley","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","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.","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.","ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 2020;39(2):89-99. doi:10.1111/cgf.13914","apa":"Schreck, C., & Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13914","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."},"title":"A practical method for animating anisotropic elastoplastic materials","author":[{"full_name":"Schreck, Camille","last_name":"Schreck","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000548709600008"]},"article_processing_charge":"No","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"7605f605acd84d0942b48bc7a1c2d72e","file_id":"8796","creator":"dernst","file_size":38969122,"date_updated":"2020-11-23T09:05:13Z","file_name":"2020_poff_revisited.pdf","date_created":"2020-11-23T09:05:13Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"publication_status":"published","issue":"2","volume":39,"ec_funded":1,"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"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.","lang":"eng"}],"month":"05","intvolume":" 39","scopus_import":"1","ddc":["000"],"date_updated":"2023-09-05T16:00:13Z","department":[{"_id":"ChWo"}],"file_date_updated":"2020-11-23T09:05:13Z","_id":"8765","status":"public","keyword":["Computer Networks and Communications"],"type":"journal_article","article_type":"original"},{"_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)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-05T15:47:50Z","ddc":["540","541"],"department":[{"_id":"StFr"}],"file_date_updated":"2020-09-17T08:59:43Z","abstract":[{"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.","lang":"eng"}],"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":[{"file_size":1904552,"date_updated":"2020-09-17T08:59:43Z","creator":"dernst","file_name":"2020_AngChemieDE_Bouchal.pdf","date_created":"2020-09-17T08:59:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8401","checksum":"7dd0a56f6bd5de08ea75b1ec388c91bc"}],"issue":"37","volume":132,"citation":{"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.","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.","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. 2020;132(37):16047-16051. doi:10.1002/ange.202005378","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202005378","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Roza","full_name":"Bouchal, Roza","last_name":"Bouchal"},{"full_name":"Li, Zhujie","last_name":"Li","first_name":"Zhujie"},{"last_name":"Bongu","full_name":"Bongu, Chandra","first_name":"Chandra"},{"last_name":"Le Vot","full_name":"Le Vot, Steven","first_name":"Steven"},{"first_name":"Romain","last_name":"Berthelot","full_name":"Berthelot, Romain"},{"last_name":"Rotenberg","full_name":"Rotenberg, Benjamin","first_name":"Benjamin"},{"last_name":"Favier","full_name":"Favier, Frederic","first_name":"Frederic"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"first_name":"Mathieu","last_name":"Salanne","full_name":"Salanne, Mathieu"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"}],"title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","oa":1,"quality_controlled":"1","publisher":"Wiley","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"},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, Ecology Letters 23 (2020) 565–574.","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.","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","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","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000507515900001"]},"author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","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"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"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","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"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.). ","oa":1,"publisher":"Wiley","quality_controlled":"1","publication":"Ecology Letters","day":"01","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-01-20T13:32:12Z","doi":"10.1111/ele.13458","date_published":"2020-03-01T00:00:00Z","page":"565-574","_id":"7343","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)"},"type":"journal_article","article_type":"letter_note","ddc":["570"],"date_updated":"2023-09-05T16:04:49Z","file_date_updated":"2020-11-19T11:27:10Z","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level."}],"intvolume":" 23","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":561749,"date_updated":"2020-11-19T11:27:10Z","creator":"dernst","file_name":"2020_EcologyLetters_Milutinovic.pdf","date_created":"2020-11-19T11:27:10Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"0cd8be386fa219db02845b7c3991ce04","file_id":"8776"}],"publication_status":"published","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13060"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/social-ants-shapes-disease-outcome/","description":"News on IST Homepage"}]},"volume":23,"issue":"3"},{"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."}],"month":"11","intvolume":" 20","scopus_import":"1","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8814","checksum":"3d87ebb8757dcd504f20c618b72e6575","success":1,"creator":"dernst","date_updated":"2020-11-26T11:46:43Z","file_size":820428,"date_created":"2020-11-26T11:46:43Z","file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"publication_status":"published","volume":20,"issue":"6","ec_funded":1,"_id":"8099","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)"},"ddc":["570"],"date_updated":"2023-09-05T16:07:08Z","file_date_updated":"2020-11-26T11:46:43Z","department":[{"_id":"BeVi"}],"publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"Molecular Ecology Resources","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-11-01T00:00:00Z","doi":"10.1111/1755-0998.13210","date_created":"2020-07-07T08:56:16Z","page":"1517-1525","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:10.1111/1755-0998.13210.","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","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.","ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. 2020;20(6):1517-1525. doi:10.1111/1755-0998.13210","apa":"Gammerdinger, W. J., Toups, M. A., & Vicoso, B. (2020). Disagreement in FST estimators: A case study from sex chromosomes. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13210","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from Sex Chromosomes.” Molecular Ecology Resources. Wiley, 2020. https://doi.org/10.1111/1755-0998.13210.","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."},"title":"Disagreement in FST estimators: A case study from sex chromosomes","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"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"external_id":{"pmid":["32543001"],"isi":["000545451200001"]},"article_processing_charge":"Yes (via OA deal)"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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.","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."},"title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","article_processing_charge":"No","external_id":{"isi":["000541488700001"],"pmid":["32390281"]},"author":[{"full_name":"Bouchal, Roza","last_name":"Bouchal","first_name":"Roza"},{"first_name":"Zhujie","full_name":"Li, Zhujie","last_name":"Li"},{"last_name":"Bongu","full_name":"Bongu, Chandra","first_name":"Chandra"},{"first_name":"Steven","last_name":"Le Vot","full_name":"Le Vot, Steven"},{"full_name":"Berthelot, Romain","last_name":"Berthelot","first_name":"Romain"},{"first_name":"Benjamin","last_name":"Rotenberg","full_name":"Rotenberg, Benjamin"},{"last_name":"Favier","full_name":"Favier, Fréderic","first_name":"Fréderic"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger"},{"first_name":"Mathieu","full_name":"Salanne, Mathieu","last_name":"Salanne"},{"full_name":"Fontaine, Olivier","last_name":"Fontaine","first_name":"Olivier"}],"oa":1,"publisher":"Wiley","quality_controlled":"1","publication":"Angewandte Chemie International Edition","day":"07","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-05-14T21:00:30Z","date_published":"2020-09-07T00:00:00Z","doi":"10.1002/anie.202005378","page":"15913-1591","_id":"7847","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":["540","546"],"date_updated":"2023-09-05T16:02:53Z","file_date_updated":"2020-09-17T08:57:16Z","department":[{"_id":"StFr"}],"oa_version":"Published Version","pmid":1,"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. "}],"intvolume":" 59","month":"09","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"7b6c2fc20e9b0ff4353352f7a7004e2d","file_id":"8400","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_AngChemieINT_Buchal.pdf","date_created":"2020-09-17T08:57:16Z","file_size":1966184,"date_updated":"2020-09-17T08:57:16Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"issue":"37","volume":59},{"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","month":"03","intvolume":" 23","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"publication_status":"published","file":[{"date_created":"2020-02-14T12:02:50Z","file_name":"2020_EcologyLetters_Rybicki.pdf","date_updated":"2020-07-14T12:47:54Z","file_size":3005474,"creator":"dernst","checksum":"372f67f2744f4b6049e9778364766c22","file_id":"7486","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"3","volume":23,"ec_funded":1,"_id":"7224","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":"2023-09-05T16:04:30Z","ddc":["000"],"department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:47:54Z","quality_controlled":"1","publisher":"Wiley","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Ecology Letters","page":"506-517","doi":"10.1111/ele.13450","date_published":"2020-03-01T00:00:00Z","date_created":"2020-01-04T11:04:30Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","grant_number":"840605"}],"citation":{"ista":"Rybicki J, Abrego N, Ovaskainen O. 2020. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 23(3), 506–517.","chicago":"Rybicki, Joel, Nerea Abrego, and Otso Ovaskainen. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13450.","ieee":"J. Rybicki, N. Abrego, and O. Ovaskainen, “Habitat fragmentation and species diversity in competitive communities,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 506–517, 2020.","short":"J. Rybicki, N. Abrego, O. Ovaskainen, Ecology Letters 23 (2020) 506–517.","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel"},{"last_name":"Abrego","full_name":"Abrego, Nerea","first_name":"Nerea"},{"full_name":"Ovaskainen, Otso","last_name":"Ovaskainen","first_name":"Otso"}],"external_id":{"isi":["000503625200001"]},"article_processing_charge":"Yes (via OA deal)","title":"Habitat fragmentation and species diversity in competitive communities"},{"volume":59,"issue":"51","related_material":{"record":[{"relation":"research_data","status":"public","id":"9780"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"publication_status":"published","month":"12","intvolume":" 59","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.202008253"}],"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."}],"department":[{"_id":"StFr"}],"date_updated":"2023-09-05T16:03:47Z","status":"public","article_type":"original","type":"journal_article","_id":"8329","date_published":"2020-12-14T00:00:00Z","doi":"10.1002/anie.202008253","date_created":"2020-09-03T16:10:56Z","page":"22943-22946","day":"14","publication":"Angewandte Chemie International Edition","isi":1,"year":"2020","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries","author":[{"full_name":"Schlemmer, Werner","last_name":"Schlemmer","first_name":"Werner"},{"last_name":"Nothdurft","full_name":"Nothdurft, Philipp","first_name":"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"},{"last_name":"Gescheidt-Demner","full_name":"Gescheidt-Demner, Georg","first_name":"Georg"},{"last_name":"Fischer","full_name":"Fischer, Roland","first_name":"Roland"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger"},{"last_name":"Kern","full_name":"Kern, Wolfgang","first_name":"Wolfgang"},{"last_name":"Spirk","full_name":"Spirk, Stefan","first_name":"Stefan"}],"article_processing_charge":"No","external_id":{"isi":["000576148700001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253.","short":"W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946.","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.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 2020;59(51):22943-22946. doi:10.1002/anie.202008253","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202008253"}},{"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-05T16:04:48Z","citation":{"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","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","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."},"title":"Social immunity modulates competition between coinfecting pathogens","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"article_processing_charge":"No","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Milutinovic","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara"},{"last_name":"Stock","full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"last_name":"Grasse","full_name":"Grasse, Anna V","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"_id":"13060","status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","day":"19","year":"2020","date_created":"2023-05-23T16:11:22Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7343"}]},"doi":"10.5061/DRYAD.CRJDFN318","date_published":"2020-12-19T00:00:00Z","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."}],"month":"12","main_file_link":[{"url":"https://doi.org/10.5061/dryad.crjdfn318","open_access":"1"}],"oa":1,"publisher":"Dryad"},{"citation":{"ama":"Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk","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.","mla":"Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure Determination. CCDC, 2020, doi: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.","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."},"date_updated":"2023-09-05T16:03:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Schlemmer, Werner","last_name":"Schlemmer","first_name":"Werner"},{"last_name":"Nothdurft","full_name":"Nothdurft, Philipp","first_name":"Philipp"},{"full_name":"Petzold, Alina","last_name":"Petzold","first_name":"Alina"},{"first_name":"Gisbert","last_name":"Riess","full_name":"Riess, Gisbert"},{"first_name":"Philipp","last_name":"Frühwirt","full_name":"Frühwirt, Philipp"},{"first_name":"Max","last_name":"Schmallegger","full_name":"Schmallegger, Max"},{"last_name":"Gescheidt-Demner","full_name":"Gescheidt-Demner, Georg","first_name":"Georg"},{"last_name":"Fischer","full_name":"Fischer, Roland","first_name":"Roland"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Kern, Wolfgang","last_name":"Kern","first_name":"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","_id":"9780","type":"research_data_reference","status":"public","year":"2020","day":"22","date_published":"2020-03-22T00:00:00Z","doi":"10.5517/ccdc.csd.cc24vsrk","related_material":{"record":[{"id":"8329","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-06T07:41:07Z","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","publisher":"CCDC","oa":1,"main_file_link":[{"open_access":"1","url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk"}],"month":"03"},{"project":[{"call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"},{"call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425","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","external_id":{"pmid":["31729777"],"isi":["000502270900001"]},"article_processing_charge":"No","author":[{"full_name":"Martín-Belmonte, Alejandro","last_name":"Martín-Belmonte","first_name":"Alejandro"},{"full_name":"Aguado, Carolina","last_name":"Aguado","first_name":"Carolina"},{"full_name":"Alfaro-Ruíz, Rocío","last_name":"Alfaro-Ruíz","first_name":"Rocío"},{"last_name":"Moreno-Martínez","full_name":"Moreno-Martínez, Ana Esther","first_name":"Ana Esther"},{"first_name":"Luis","last_name":"De La Ossa","full_name":"De La Ossa, Luis"},{"last_name":"Martínez-Hernández","full_name":"Martínez-Hernández, José","first_name":"José"},{"first_name":"Alain","last_name":"Buisson","full_name":"Buisson, Alain"},{"first_name":"Simon","full_name":"Früh, Simon","last_name":"Früh"},{"full_name":"Bettler, Bernhard","last_name":"Bettler","first_name":"Bernhard"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 2020;30(3):554-575. doi:10.1111/bpa.12802","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. Wiley. https://doi.org/10.1111/bpa.12802","chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology. Wiley, 2020. https://doi.org/10.1111/bpa.12802.","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."},"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2019-12-22T23:00:43Z","doi":"10.1111/bpa.12802","date_published":"2020-05-01T00:00:00Z","page":"554-575","publication":"Brain Pathology","day":"01","year":"2020","has_accepted_license":"1","isi":1,"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","_id":"7207","file_date_updated":"2020-09-22T09:47:19Z","department":[{"_id":"RySh"}],"ddc":["570"],"date_updated":"2023-09-06T14:48:01Z","intvolume":" 30","month":"05","scopus_import":"1","pmid":1,"oa_version":"Published Version","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"}],"ec_funded":1,"volume":30,"issue":"3","language":[{"iso":"eng"}],"file":[{"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","success":1,"checksum":"549cc1b18f638a21d17a939ba5563fa9","file_id":"8554","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["17503639"],"issn":["10156305"]}},{"volume":33,"related_material":{"record":[{"id":"13067","status":"public","relation":"research_data"}]},"issue":"3","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"publication_status":"published","file":[{"success":1,"file_id":"8553","checksum":"7534ff0839709c0c5265c12d29432f03","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_EvolBiology_Johannesson.pdf","date_created":"2020-09-22T09:42:18Z","file_size":885611,"date_updated":"2020-09-22T09:42:18Z","creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 33","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"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"NiBa"}],"file_date_updated":"2020-09-22T09:42:18Z","date_updated":"2023-09-06T14:48:57Z","ddc":["570"],"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)"},"status":"public","_id":"7205","page":"342-351","date_published":"2020-03-01T00:00:00Z","doi":"10.1111/jeb.13570","date_created":"2019-12-22T23:00:43Z","isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Journal of Evolutionary Biology","publisher":"Wiley","quality_controlled":"1","oa":1,"author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Zuzanna","full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"article_processing_charge":"No","external_id":{"pmid":["31724256"],"isi":["000500954800001"]},"title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","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.","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","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","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"7227","status":"public","type":"book_chapter","date_updated":"2023-09-06T14:54:36Z","department":[{"_id":"CaHe"}],"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation."}],"month":"06","intvolume":" 136","alternative_title":["Current Topics in Developmental Biology"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00702153"]},"publication_status":"published","volume":136,"ec_funded":1,"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2646861A-B435-11E9-9278-68D0E5697425","name":"Control of embryonic cleavage pattern","grant_number":"I03601"},{"_id":"2608FC64-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Control of epithelial cell layer spreading in zebrafish","grant_number":"I03196"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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."},"title":"Zebrafish gastrulation: Putting fate in motion","author":[{"first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"isi":["000611830600013"],"pmid":["31959295"]},"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).","quality_controlled":"1","publisher":"Elsevier","day":"01","publication":"Gastrulation: From Embryonic Pattern to Form","isi":1,"year":"2020","doi":"10.1016/bs.ctdb.2019.10.009","date_published":"2020-06-01T00:00:00Z","date_created":"2020-01-05T23:00:46Z","page":"343-375"},{"abstract":[{"lang":"eng","text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154"}],"scopus_import":"1","intvolume":" 15","month":"01","publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"language":[{"iso":"eng"}],"issue":"1","volume":15,"_id":"7417","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-06T15:23:04Z","department":[{"_id":"JiFr"}],"oa":1,"publisher":"Informa UK Limited","quality_controlled":"1","year":"2020","isi":1,"publication":"Plant Signaling & Behavior","day":"01","date_created":"2020-01-30T10:14:14Z","doi":"10.1080/15592324.2019.1687185","date_published":"2020-01-01T00:00:00Z","article_number":"e1687185","citation":{"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.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 15(1), e1687185.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:10.1080/15592324.2019.1687185.","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","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.","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling & Behavior 15 (2020)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000494907500001"],"pmid":["31696770"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A","last_name":"Sinclair","first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gille, S.","last_name":"Gille","first_name":"S."},{"first_name":"M.","last_name":"Pauly","full_name":"Pauly, M."},{"last_name":"Krämer","full_name":"Krämer, U.","first_name":"U."}],"title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli"},{"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","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."},"title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"external_id":{"isi":["000529483000001"],"arxiv":["1809.03971"]},"article_processing_charge":"Yes (via OA deal)","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Communications in Mathematical Physics","isi":1,"has_accepted_license":"1","year":"2020","date_published":"2020-09-01T00:00:00Z","doi":"10.1007/s00220-019-03657-4","date_created":"2019-03-28T10:21:15Z","page":"1203-1278","_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)"},"ddc":["530","510"],"date_updated":"2023-09-07T12:54:12Z","department":[{"_id":"LaEr"}],"file_date_updated":"2020-11-18T11:14:37Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969)."}],"month":"09","intvolume":" 378","scopus_import":"1","file":[{"file_name":"2020_CommMathPhysics_Erdoes.pdf","date_created":"2020-11-18T11:14:37Z","creator":"dernst","file_size":2904574,"date_updated":"2020-11-18T11:14:37Z","success":1,"file_id":"8771","checksum":"c3a683e2afdcea27afa6880b01e53dc2","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"6179","relation":"dissertation_contains"}]},"volume":378,"ec_funded":1},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"31","year":"2020","has_accepted_license":"1","date_created":"2020-04-02T06:40:23Z","doi":"10.15479/AT:ISTA:7629","date_published":"2020-03-31T00:00:00Z","page":"154","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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."},"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","article_processing_charge":"No","author":[{"last_name":"Forkert","full_name":"Forkert, Dominik L","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"month":"03","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_Forkert_PDFA.pdf","date_created":"2020-04-14T10:47:59Z","file_size":3297129,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_id":"7657","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_source.zip","date_updated":"2020-07-14T12:48:01Z","file_size":1063908,"creator":"dernst","file_id":"7658","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"_id":"7629","status":"public","type":"dissertation","ddc":["510"],"date_updated":"2023-09-07T13:03:12Z","supervisor":[{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"}],"file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"JaMa"}]},{"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2020","day":"20","page":"158","doi":"10.15479/AT:ISTA:8574","date_published":"2020-09-20T00:00:00Z","date_created":"2020-09-28T07:33:38Z","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.","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","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Szep","full_name":"Szep, Eniko","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Local adaptation in metapopulations","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. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_identifier":{"eissn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"thesis_EnikoSzep_final.pdf","date_created":"2020-09-28T07:25:35Z","file_size":6354833,"date_updated":"2020-09-28T07:25:35Z","creator":"dernst","success":1,"file_id":"8575","checksum":"20e71f015fbbd78fea708893ad634ed0","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"file_name":"thesisFiles_EnikoSzep.zip","date_created":"2020-09-28T07:25:37Z","file_size":23020401,"date_updated":"2020-09-28T07:25:37Z","creator":"dernst","file_id":"8576","checksum":"a8de2c14a1bb4e53c857787efbb289e1","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"}],"language":[{"iso":"eng"}],"_id":"8574","type":"dissertation","status":"public","supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_updated":"2023-09-07T13:11:39Z","ddc":["570"],"file_date_updated":"2020-09-28T07:25:37Z","department":[{"_id":"NiBa"}]},{"year":"2020","has_accepted_license":"1","day":"24","page":"148","date_created":"2020-02-24T09:17:27Z","doi":"10.15479/AT:ISTA:7514","date_published":"2020-02-24T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","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","article_processing_charge":"No","author":[{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Mayer","full_name":"Mayer, Simon"}],"title":"The free energy of a dilute two-dimensional Bose gas","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"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"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_id":"7516","creator":"dernst","file_size":2028038,"date_updated":"2020-07-14T12:47:59Z","file_name":"thesis_source.zip","date_created":"2020-02-24T09:15:16Z"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7524"}]},"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","alternative_title":["ISTA Thesis"],"month":"02","date_updated":"2023-09-07T13:12:42Z","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"ddc":["510"],"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"_id":"7514","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"},{"publisher":"Institute of Science and Technology Austria","oa":1,"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.","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8353","date_created":"2020-09-09T14:27:01Z","page":"191","day":"09","has_accepted_license":"1","year":"2020","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","author":[{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia","last_name":"Steiner"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","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.","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.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","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."},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"None","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"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"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8284","status":"public"}]},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"8354","checksum":"2388d7e6e7a4d364c096fa89f305c3de","file_size":117547589,"date_updated":"2021-09-16T12:40:56Z","creator":"jsteiner","file_name":"Thesis_Julia_Steiner_pdfA.pdf","date_created":"2020-09-09T14:22:35Z"},{"checksum":"ba112f957b7145462d0ab79044873ee9","file_id":"8355","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Thesis_Julia_Steiner.docx","date_created":"2020-09-09T14:23:25Z","file_size":223328668,"date_updated":"2020-09-15T08:48:37Z","creator":"jsteiner"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","_id":"8353","file_date_updated":"2021-09-16T12:40:56Z","department":[{"_id":"LeSa"}],"ddc":["572"],"supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:14:09Z"},{"title":"Novel insights into PIN polarity regulation during Arabidopsis development","author":[{"first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","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","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."},"date_published":"2020-09-30T00:00:00Z","doi":"10.15479/AT:ISTA:8589","date_created":"2020-09-30T14:50:51Z","page":"164","day":"30","has_accepted_license":"1","year":"2020","publisher":"Institute of Science and Technology Austria","oa":1,"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.","file_date_updated":"2021-10-01T13:33:02Z","department":[{"_id":"JiFr"}],"ddc":["580"],"supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:13:05Z","status":"public","type":"dissertation","_id":"8589","related_material":{"record":[{"status":"public","id":"7643","relation":"part_of_dissertation"}]},"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"8590","checksum":"c4bda1947d4c09c428ac9ce667b02327","file_size":49198118,"date_updated":"2020-09-30T14:50:20Z","creator":"dernst","file_name":"2020_Han_Thesis.docx","date_created":"2020-09-30T14:50:20Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"8591","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","creator":"dernst","file_size":15513963,"date_updated":"2021-10-01T13:33:02Z","file_name":"2020_Han_Thesis.pdf","date_created":"2020-09-30T14:49:59Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"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.","lang":"eng"}]},{"citation":{"ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","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.","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"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"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","article_number":"e59407","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"year":"2020","has_accepted_license":"1","isi":1,"publication":"eLife","day":"31","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","date_updated":"2023-09-07T13:14:08Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2020-08-24T13:31:53Z","_id":"8284","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","publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8289","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_eLife_Steiner.pdf","date_created":"2020-08-24T13:31:53Z","creator":"cziletti","file_size":7320493,"date_updated":"2020-08-24T13:31:53Z"}],"volume":9,"related_material":{"record":[{"relation":"dissertation_contains","id":"8353","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release"}]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 9","month":"07"},{"alternative_title":["ISTA Thesis"],"month":"07","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"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7675","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7569"},{"relation":"part_of_dissertation","id":"7652","status":"public"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8176","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-07-27T12:00:07Z","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","date_updated":"2020-07-27T12:00:07Z","file_size":16638998,"creator":"rgrah"},{"file_id":"8177","relation":"main_file","access_level":"closed","content_type":"application/zip","file_name":"Thesis_new.zip","date_created":"2020-07-27T12:02:23Z","creator":"rgrah","file_size":347459978,"date_updated":"2020-07-30T13:04:55Z"}],"type":"dissertation","status":"public","_id":"8155","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-30T13:04:55Z","date_updated":"2023-09-07T13:13:27Z","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"ddc":["530","570"],"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","page":"310","date_created":"2020-07-23T09:51:28Z","doi":"10.15479/AT:ISTA:8155","date_published":"2020-07-24T00:00:00Z","year":"2020","has_accepted_license":"1","day":"24","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"article_processing_charge":"No","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"}],"title":"Gene regulation across scales – how biophysical constraints shape evolution","citation":{"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.","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.","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","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). ","page":"37-40","date_created":"2020-04-06T10:06:40Z","doi":"10.1104/pp.20.00212","date_published":"2020-05-08T00:00:00Z","year":"2020","isi":1,"publication":"Plant Physiology","day":"08","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"article_processing_charge":"No","external_id":{"isi":["000536641800018"],"pmid":["32107280"]},"author":[{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","full_name":"Rakusova, Hana","last_name":"Rakusova"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","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.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","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.","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","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","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.20.00212"}],"scopus_import":"1","intvolume":" 183","month":"05","pmid":1,"oa_version":"Published Version","ec_funded":1,"issue":"5","related_material":{"record":[{"relation":"dissertation_contains","id":"8589","status":"public"}]},"volume":183,"publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"language":[{"iso":"eng"}],"article_type":"letter_note","type":"journal_article","status":"public","_id":"7643","department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T13:13:04Z"},{"month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"date_created":"2020-04-23T10:12:51Z","date_published":"2020-04-09T00:00:00Z","doi":"10.1101/2020.04.08.029405","related_material":{"record":[{"relation":"dissertation_contains","id":"8155","status":"public"}]},"publication":"bioRxiv","language":[{"iso":"eng"}],"day":"09","year":"2020","publication_status":"published","status":"public","project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"type":"preprint","_id":"7675","title":"Normative models of enhancer function","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 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","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi: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.","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."},"date_updated":"2023-09-07T13:13:26Z"},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2020-02-06T14:56:53Z","date_published":"2020-02-10T00:00:00Z","doi":"10.15479/AT:ISTA:7460","page":"155","day":"10","year":"2020","has_accepted_license":"1","title":"The hole system of triangulated shapes","article_processing_charge":"No","author":[{"first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297","full_name":"Ölsböck, Katharina","last_name":"Ölsböck"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460."},"month":"02","alternative_title":["ISTA Thesis"],"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"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"6608","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7461","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","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"},{"file_name":"latex-files.zip","date_created":"2020-02-06T14:52:45Z","file_size":122103715,"date_updated":"2020-07-14T12:47:58Z","creator":"koelsboe","file_id":"7462","checksum":"7a52383c812b0be64d3826546509e5a4","description":"latex source files, figures","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"status":"public","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","_id":"7460","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:58Z","ddc":["514"],"date_updated":"2023-09-07T13:15:30Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}]},{"_id":"7896","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","date_updated":"2023-09-07T13:15:55Z","supervisor":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:48:04Z","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","alternative_title":["ISTA Thesis"],"month":"05","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7897","checksum":"b39e2e1c376f5819b823fb7077491c64","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":1622742,"date_created":"2020-05-26T14:08:13Z","file_name":"2020_Thesis_Kamath.pdf"},{"checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","file_id":"7898","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2020-05-26T14:08:23Z","file_name":"Thesis_Kamath.zip","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":15301529}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"6677","status":"public"}]},"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"citation":{"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","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.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"}],"title":"On the average-case hardness of total search problems","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"25","page":"126","date_created":"2020-05-26T14:08:55Z","date_published":"2020-05-25T00:00:00Z","doi":"10.15479/AT:ISTA:7896"},{"article_number":"1716-1725","title":"Localizing grouped instances for efficient detection in low-resource scenarios","article_processing_charge":"No","external_id":{"arxiv":["2004.12623"]},"author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","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.","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."},"oa":1,"quality_controlled":"1","publisher":"IEEE","date_created":"2020-06-07T22:00:53Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1109/WACV45572.2020.9093288","publication":"IEEE Winter Conference on Applications of Computer Vision","day":"01","year":"2020","status":"public","conference":{"start_date":"2020-03-01","end_date":"2020-03-05","location":" Snowmass Village, CO, United States","name":"WACV: Winter Conference on Applications of Computer Vision"},"type":"conference","_id":"7936","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:17Z","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/2004.12623","open_access":"1"}],"scopus_import":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."}],"related_material":{"record":[{"id":"8331","status":"deleted","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"8390"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781728165530"]}},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/2008.11995"}],"scopus_import":"1","month":"03","publication_status":"published","publication_identifier":{"isbn":["9781728165530"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8331","status":"deleted"},{"relation":"dissertation_contains","id":"8390","status":"public"}]},"_id":"7937","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","location":"Snowmass Village, CO, United States","end_date":"2020-03-05","start_date":"2020-03-01"},"type":"conference","status":"public","date_updated":"2023-09-07T13:16:17Z","department":[{"_id":"ChLa"}],"oa":1,"publisher":"IEEE","quality_controlled":"1","year":"2020","publication":"2020 IEEE Winter Conference on Applications of Computer Vision","day":"01","date_created":"2020-06-07T22:00:53Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1109/WACV45572.2020.9093635","article_number":"2180-2189","citation":{"mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” 2020 IEEE Winter Conference on Applications of Computer Vision, 2180–2189, IEEE, 2020, doi:10.1109/WACV45572.2020.9093635.","short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","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.","ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093635","apa":"Royer, A., & Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In 2020 IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093635","chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093635.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2008.11995"]},"author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","last_name":"Royer"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"title":"A flexible selection scheme for minimum-effort transfer learning"},{"department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T13:16:18Z","type":"conference","conference":{"start_date":"2020-10-26","location":"Nancy, France","end_date":"2020-10-30","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"status":"public","_id":"8193","related_material":{"record":[{"id":"8390","status":"public","relation":"dissertation_contains"}]},"volume":30,"publication_identifier":{"eissn":["23340843"],"issn":["23340835"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 30","abstract":[{"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.","lang":"eng"}],"oa_version":"None","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"first_name":"Deep","last_name":"Karkhanis","full_name":"Karkhanis, Deep"},{"full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","last_name":"Royer","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705"}],"article_processing_charge":"No","title":"Multiple-environment Markov decision processes: Efficient analysis and applications","citation":{"ama":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. Multiple-environment Markov decision processes: Efficient analysis and applications. In: Proceedings of the 30th International Conference on Automated Planning and Scheduling. Vol 30. Association for the Advancement of Artificial Intelligence; 2020:48-56.","apa":"Chatterjee, K., Chmelik, M., Karkhanis, D., Novotný, P., & Royer, A. (2020). Multiple-environment Markov decision processes: Efficient analysis and applications. In Proceedings of the 30th International Conference on Automated Planning and Scheduling (Vol. 30, pp. 48–56). Nancy, France: Association for the Advancement of Artificial Intelligence.","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"48-56","date_published":"2020-06-01T00:00:00Z","date_created":"2020-08-02T22:00:58Z","year":"2020","day":"01","publication":"Proceedings of the 30th International Conference on Automated Planning and Scheduling","publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1","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."},{"editor":[{"last_name":"Singh","full_name":"Singh, Richa","first_name":"Richa"},{"full_name":"Vatsa, Mayank","last_name":"Vatsa","first_name":"Mayank"},{"last_name":"Patel","full_name":"Patel, Vishal M.","first_name":"Vishal M."},{"full_name":"Ratha, Nalini","last_name":"Ratha","first_name":"Nalini"}],"title":"XGAN: Unsupervised image-to-image translation for many-to-many mappings","external_id":{"arxiv":["1711.05139"]},"article_processing_charge":"No","author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","last_name":"Royer","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie"},{"last_name":"Bousmalis","full_name":"Bousmalis, Konstantinos","first_name":"Konstantinos"},{"first_name":"Stephan","last_name":"Gouws","full_name":"Gouws, Stephan"},{"last_name":"Bertsch","full_name":"Bertsch, Fred","first_name":"Fred"},{"full_name":"Mosseri, Inbar","last_name":"Mosseri","first_name":"Inbar"},{"first_name":"Forrester","last_name":"Cole","full_name":"Cole, Forrester"},{"last_name":"Murphy","full_name":"Murphy, Kevin","first_name":"Kevin"}],"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.","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.","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","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."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","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","publication":"Domain Adaptation for Visual Understanding","day":"08","year":"2020","status":"public","type":"book_chapter","_id":"8092","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:18Z","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.05139"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8331","status":"deleted"},{"relation":"dissertation_contains","status":"public","id":"8390"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030306717"]}},{"file_date_updated":"2020-07-14T12:48:05Z","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"ddc":["516","514"],"date_updated":"2023-09-07T13:17:37Z","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"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","license":"https://creativecommons.org/licenses/by-sa/4.0/","related_material":{"record":[{"status":"public","id":"7950","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5986","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"df688bc5a82b50baee0b99d25fc7b7f0","file_id":"7945","date_updated":"2020-07-14T12:48:05Z","file_size":13661779,"creator":"zmasarov","date_created":"2020-06-08T00:34:00Z","file_name":"THESIS_Zuzka_Masarova.pdf"},{"date_updated":"2020-07-14T12:48:05Z","file_size":32184006,"creator":"zmasarov","date_created":"2020-06-08T00:35:30Z","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"45341a35b8f5529c74010b7af43ac188","file_id":"7946"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-005-3"]},"month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars."}],"title":"Reconfiguration problems","article_processing_charge":"No","author":[{"last_name":"Masárová","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","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","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","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."},"date_created":"2020-06-08T00:49:46Z","doi":"10.15479/AT:ISTA:7944","date_published":"2020-06-09T00:00:00Z","page":"160","day":"09","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"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."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"month":"04","intvolume":" 152","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"16","related_material":{"record":[{"status":"public","id":"8958","relation":"dissertation_contains"}]},"volume":152,"ec_funded":1,"_id":"8587","article_type":"original","type":"journal_article","status":"public","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"date_updated":"2023-09-07T13:16:42Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"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.","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"isi":1,"year":"2020","day":"27","publication":"The Journal of Chemical Physics","doi":"10.1063/1.5144759","date_published":"2020-04-27T00:00:00Z","date_created":"2020-09-30T10:33:17Z","article_number":"164302","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"},{"name":"A path-integral approach to composite impurities","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"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.","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).","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","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang","last_name":"Li","full_name":"Li, Xiang"},{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu"},{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin"},{"first_name":"Richard","full_name":"Schmidt, Richard","last_name":"Schmidt"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Deuchert","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas"}],"article_processing_charge":"No","external_id":{"isi":["000530448300001"],"arxiv":["1912.02658"]},"title":"Intermolecular forces and correlations mediated by a phonon bath"},{"file_date_updated":"2021-09-16T12:49:12Z","department":[{"_id":"MaLo"}],"supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"date_updated":"2023-09-07T13:17:06Z","ddc":["570"],"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)"},"status":"public","_id":"8341","related_material":{"record":[{"status":"public","id":"7580","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"8342","checksum":"70871b335a595252a66c6bbf0824fb02","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","date_created":"2020-09-08T09:00:29Z","file_size":65246782,"date_updated":"2021-09-16T12:49:12Z","creator":"dernst"},{"file_size":31259058,"date_updated":"2021-09-16T12:49:12Z","creator":"dernst","file_name":"2020_Urban_Bezeljak_Thesis.pdf","date_created":"2020-09-08T09:00:27Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"8343","checksum":"59a62275088b00b7241e6ff4136434c7"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","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."}],"oa_version":"Published Version","author":[{"id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban","last_name":"Bezeljak","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631"}],"article_processing_charge":"No","title":"In vitro reconstitution of a Rab activation switch","citation":{"mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","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","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.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"215","date_published":"2020-09-08T00:00:00Z","doi":"10.15479/AT:ISTA:8341","date_created":"2020-09-08T08:53:53Z","has_accepted_license":"1","year":"2020","day":"08","publisher":"Institute of Science and Technology Austria","oa":1,"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."},{"oa":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","date_created":"2020-03-12T05:32:26Z","date_published":"2020-03-24T00:00:00Z","doi":"10.1073/pnas.1921027117","page":"6504-6549","publication":"Proceedings of the National Academy of Sciences","day":"24","year":"2020","isi":1,"project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"title":"Stochastic activation and bistability in a Rab GTPase regulatory network","article_processing_charge":"No","external_id":{"isi":["000521821800040"]},"author":[{"last_name":"Bezeljak","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loya, Hrushikesh","last_name":"Loya","first_name":"Hrushikesh"},{"last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Timothy E.","last_name":"Saunders","full_name":"Saunders, Timothy E."},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117","apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117","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.","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."},"intvolume":" 117","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"scopus_import":"1","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"}],"issue":"12","volume":117,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"8341","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","type":"journal_article","article_type":"original","_id":"7580","department":[{"_id":"MaLo"},{"_id":"CaBe"}],"date_updated":"2023-09-07T13:17:06Z"},{"oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"26","page":"xviii+120","date_created":"2020-06-26T10:00:36Z","date_published":"2020-06-26T00:00:00Z","doi":"10.15479/AT:ISTA:8032","citation":{"mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032","apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032","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.","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.","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Huszár","orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf"}],"title":"Combinatorial width parameters for 3-dimensional manifolds","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"}],"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-006-0"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3","file_id":"8034","creator":"khuszar","file_size":2637562,"date_updated":"2020-07-14T12:48:08Z","file_name":"Kristof_Huszar-Thesis.pdf","date_created":"2020-06-26T10:03:58Z"},{"date_created":"2020-06-26T10:10:06Z","file_name":"Kristof_Huszar-Thesis-source.zip","date_updated":"2020-07-14T12:48:08Z","file_size":7163491,"creator":"khuszar","checksum":"d5f8456202b32f4a77552ef47a2837d1","file_id":"8035","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"6556","status":"public"},{"status":"public","id":"7093","relation":"dissertation_contains"}]},"_id":"8032","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","date_updated":"2023-09-07T13:18:27Z","supervisor":[{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"first_name":"Jonathan","last_name":"Spreer","full_name":"Spreer, Jonathan"}],"ddc":["514"],"file_date_updated":"2020-07-14T12:48:08Z","department":[{"_id":"UlWa"}]},{"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"external_id":{"isi":["000695276000014"]},"article_processing_charge":"No","author":[{"last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"title":"Refinement for structured concurrent programs","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.","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.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","page":"275-298","date_created":"2020-08-03T11:45:35Z","doi":"10.1007/978-3-030-53288-8_14","date_published":"2020-07-14T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"Computer Aided Verification","day":"14","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","_id":"8195","file_date_updated":"2020-08-06T08:14:54Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T13:18:00Z","ddc":["000"],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 12224","month":"07","abstract":[{"lang":"eng","text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier."}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"volume":12224,"publication_status":"published","publication_identifier":{"isbn":["9783030532871"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783030532888"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8201","file_size":804237,"date_updated":"2020-08-06T08:14:54Z","creator":"dernst","file_name":"2020_LNCS_Kragl.pdf","date_created":"2020-08-06T08:14:54Z"}]},{"oa_version":"Published Version","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."}],"month":"06","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3385412.3385980","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450376136"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"8332","status":"public"}]},"_id":"8012","status":"public","type":"conference","conference":{"location":"London, United Kingdom","end_date":"2020-06-20","start_date":"2020-06-15","name":"PLDI: Programming Language Design and Implementation"},"date_updated":"2023-09-07T13:18:00Z","department":[{"_id":"ToHe"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"day":"01","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","isi":1,"year":"2020","doi":"10.1145/3385412.3385980","date_published":"2020-06-01T00:00:00Z","date_created":"2020-06-25T11:40:16Z","page":"227-242","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. Inductive sequentialization of asynchronous programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:227-242. doi:10.1145/3385412.3385980","apa":"Kragl, B., Enea, C., Henzinger, T. A., Mutluergil, S. O., & Qadeer, S. (2020). Inductive sequentialization of asynchronous programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 227–242). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385980","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.","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.","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.","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."},"title":"Inductive sequentialization of asynchronous programs","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"full_name":"Enea, Constantin","last_name":"Enea","first_name":"Constantin"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","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"}],"article_processing_charge":"No","external_id":{"isi":["000614622300016"]}},{"page":"135","doi":"10.15479/AT:ISTA:8358","date_published":"2020-09-10T00:00:00Z","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.","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":{"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.","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.","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.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"7572","relation":"dissertation_contains"},{"relation":"part_of_dissertation","id":"7197","status":"public"}]},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-009-1"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_created":"2020-09-10T12:11:29Z","file_name":"phd_thesis_pcaldas.pdf","creator":"pcaldas","date_updated":"2020-09-10T12:11:29Z","file_size":141602462,"file_id":"8364","checksum":"882f93fe9c351962120e2669b84bf088","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_id":"8365","file_size":450437458,"date_updated":"2020-09-11T07:48:10Z","creator":"pcaldas","file_name":"phd_thesis_latex_pcaldas.zip","date_created":"2020-09-10T12:18:17Z"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"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","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version","department":[{"_id":"MaLo"}],"file_date_updated":"2020-09-11T07:48:10Z","supervisor":[{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"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"},{"status":"public","conference":{"name":"ESA: Annual European Symposium on Algorithms","start_date":"2020-09-07","location":"Virtual, Online; Pisa, Italy","end_date":"2020-09-09"},"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)"},"type":"conference","_id":"8703","department":[{"_id":"HeEd"}],"file_date_updated":"2020-10-27T14:31:52Z","ddc":["000"],"date_updated":"2023-09-07T13:29:00Z","intvolume":" 173","month":"08","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"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. ","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/3.0/","ec_funded":1,"volume":173,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9056"}]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8712","checksum":"fe0f7c49a99ed870c671b911e10d5496","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_LIPIcs_Osang.pdf","date_created":"2020-10-27T14:31:52Z","creator":"cziletti","file_size":733291,"date_updated":"2020-10-27T14:31:52Z"}],"publication_status":"published","publication_identifier":{"issn":["18688969"],"isbn":["9783959771627"]},"project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"}],"article_number":"75","title":"Generalizing CGAL periodic Delaunay triangulations","article_processing_charge":"No","author":[{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang"},{"last_name":"Rouxel-Labbé","full_name":"Rouxel-Labbé, Mael","first_name":"Mael"},{"first_name":"Monique","last_name":"Teillaud","full_name":"Teillaud, Monique"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","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","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","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.","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.","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."},"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"},{"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"ChLa"}],"title":"Functional vs. parametric equivalence of ReLU networks","author":[{"last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T13:29:50Z","citation":{"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.","short":"M. Phuong, C. Lampert, 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.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020.","ista":"Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020."},"status":"public","type":"conference","conference":{"start_date":"2020-04-27","end_date":"2020-04-30","location":"Online","name":"ICLR: International Conference on Learning Representations"},"_id":"7481","related_material":{"record":[{"id":"9418","status":"public","relation":"dissertation_contains"}],"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","file":[{"file_id":"7482","checksum":"8d372ea5defd8cb8fdc430111ed754a9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"main.pdf","date_created":"2020-02-11T09:07:27Z","creator":"bphuong","file_size":405469,"date_updated":"2020-07-14T12:47:59Z"}],"day":"26","publication":"8th International Conference on Learning Representations","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_status":"published","year":"2020","month":"04","quality_controlled":"1","oa":1,"oa_version":"Published Version","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"}]}]