[{"date_updated":"2023-09-27T12:26:03Z","supervisor":[{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"ddc":["571"],"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:46:04Z","_id":"324","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","pubrep_id":"997","status":"public","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","checksum":"8e163ae9e927401b9fa7c1b3e6a3631a","file_id":"5046","creator":"system","date_updated":"2020-07-14T12:46:04Z","file_size":8719458,"date_created":"2018-12-12T10:13:58Z","file_name":"IST-2018-997-v1+1_Thesis_chong_a.pdf"},{"creator":"dernst","date_updated":"2020-07-14T12:46:04Z","file_size":47841940,"date_created":"2019-04-05T09:25:26Z","file_name":"2018_Thesis_chong_source.pages","access_level":"closed","relation":"source_file","content_type":"application/octet-stream","file_id":"6221","checksum":"f7d7260029a5fbb5c982db61328ade52"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1117","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"749"}]},"abstract":[{"text":"Neuronal networks in the brain consist of two main types of neuron, glutamatergic principal neurons and GABAergic interneurons. Although these interneurons only represent 10–20% of the whole population, they mediate feedback and feedforward inhibition and are involved in the generation of high-frequency network oscillations. A hallmark functional property of GABAergic interneurons, especially of the parvalbumin‑expressing (PV+) subtypes, is the speed of signaling at their output synapse across species and brain regions. Several molecular and subcellular factors may underlie the submillisecond signaling at GABAergic synapses. Such as the selective use of P/Q type Ca2+ channels and the tight coupling between Ca2+ channels and Ca2+ sensors of exocytosis. However, whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Besides, these interneurons are mainly show depression in response to train of stimuli. How could they keep sufficient release to control the activity of postsynaptic principal neurons during high network activity, is largely elusive. For my Ph.D. work, we firstly examined the Ca2+ sensor of exocytosis at the GABAergic basket cell (BC) to Purkinje cell (PC) synapse in the cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ~10% compared to the wild-type control, identifying Syt2 as the major Ca2+ sensor at BC‑PC synapses. Differential adenovirus-mediated rescue revealed Syt2 triggered release with shorter latency and higher temporal precision, and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as the release sensor at BC–PC synapse ensures fast feedforward inhibition in cerebellar microcircuits. Additionally, we tested the function of another synaptotagmin member, Syt7, for inhibitory synaptic transmission at the BC–PC synapse. Syt7 is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, it is strongly expressed in fast-spiking, PV+ GABAergic interneurons and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. How could Syt7, a facilitation sensor, contribute to the depressed inhibitory synaptic transmission needs to be further investigated and understood. Our results indicated that at the BC–PC synapse, Syt7 contributes to asynchronous release, pool replenishment and facilitation. In combination, these three effects ensure efficient transmitter release during high‑frequency activity and guarantee frequency independence of inhibition. Taken together, our results confirmed that Syt2, which has the fastest kinetic properties among all synaptotagmin members, is mainly used by the inhibitory BC‑PC synapse for synaptic transmission, contributing to the speed and temporal precision of transmitter release. Furthermore, we showed that Syt7, another highly expressed synaptotagmin member in the output synapses of cerebellar BCs, is used for ensuring efficient inhibitor synaptic transmission during high activity.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","citation":{"ista":"Chen C. 2018. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria.","chicago":"Chen, Chong. “Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_997.","ieee":"C. Chen, “Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release,” Institute of Science and Technology Austria, 2018.","short":"C. Chen, Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release, Institute of Science and Technology Austria, 2018.","ama":"Chen C. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. 2018. doi:10.15479/AT:ISTA:th_997","apa":"Chen, C. (2018). Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_997","mla":"Chen, Chong. Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_997."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Chen","full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"}],"publist_id":"7541","title":"Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release","year":"2018","has_accepted_license":"1","day":"01","page":"110","date_created":"2018-12-11T11:45:49Z","doi":"10.15479/AT:ISTA:th_997","date_published":"2018-03-01T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria"},{"ddc":["514","516"],"date_updated":"2023-09-27T12:29:57Z","file_date_updated":"2020-07-14T12:47:58Z","department":[{"_id":"UlWa"}],"_id":"742","status":"public","pubrep_id":"912","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"kschuh","date_updated":"2020-07-14T12:47:58Z","file_size":412486,"date_created":"2019-01-15T13:44:05Z","file_name":"s10711-017-0291-4.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5835","checksum":"d2f70fc132156504aa4c626aa378a7ab"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":195,"related_material":{"record":[{"id":"1378","status":"public","relation":"earlier_version"}]},"issue":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We give a detailed and easily accessible proof of Gromov’s Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map (Formula presented.) there exists a point (Formula presented.) that is contained in the images of a positive fraction (Formula presented.) of the d-cells of X. More generally, the conclusion holds if (Formula presented.) is replaced by any d-dimensional piecewise-linear manifold M, with a constant (Formula presented.) that depends only on d and on the expansion properties of X, but not on M."}],"month":"08","intvolume":" 195","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Dotterrer D, Kaufman T, Wagner U. 2018. On expansion and topological overlap. Geometriae Dedicata. 195(1), 307–317.","chicago":"Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological Overlap.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0291-4.","apa":"Dotterrer, D., Kaufman, T., & Wagner, U. (2018). On expansion and topological overlap. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0291-4","ama":"Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. Geometriae Dedicata. 2018;195(1):307–317. doi:10.1007/s10711-017-0291-4","short":"D. Dotterrer, T. Kaufman, U. Wagner, Geometriae Dedicata 195 (2018) 307–317.","ieee":"D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” Geometriae Dedicata, vol. 195, no. 1. Springer, pp. 307–317, 2018.","mla":"Dotterrer, Dominic, et al. “On Expansion and Topological Overlap.” Geometriae Dedicata, vol. 195, no. 1, Springer, 2018, pp. 307–317, doi:10.1007/s10711-017-0291-4."},"title":"On expansion and topological overlap","author":[{"full_name":"Dotterrer, Dominic","last_name":"Dotterrer","first_name":"Dominic"},{"first_name":"Tali","last_name":"Kaufman","full_name":"Kaufman, Tali"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"publist_id":"6925","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000437122700017"]},"project":[{"_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","grant_number":"PP00P2_138948"}],"day":"01","publication":"Geometriae Dedicata","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1007/s10711-017-0291-4","date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:48:16Z","page":"307–317","quality_controlled":"1","publisher":"Springer","oa":1},{"date_updated":"2023-10-10T13:11:29Z","ddc":["510"],"file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"_id":"70","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["1980-0436"]},"publication_status":"published","file":[{"checksum":"2ded46aa284a836a8cbb34133a64f1cb","file_id":"5981","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-14T09:44:10Z","file_name":"2018_ALEA_Nejjar.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:46Z","file_size":394851}],"language":[{"iso":"eng"}],"issue":"2","volume":15,"ec_funded":1,"abstract":[{"text":"We consider the totally asymmetric simple exclusion process in a critical scaling parametrized by a≥0, which creates a shock in the particle density of order aT−1/3, T the observation time. When starting from step initial data, we provide bounds on the limiting law which in particular imply that in the double limit lima→∞limT→∞ one recovers the product limit law and the degeneration of the correlation length observed at shocks of order 1. This result is shown to apply to a general last-passage percolation model. We also obtain bounds on the two-point functions of several airy processes.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 15","citation":{"ista":"Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. 15(2), 1311–1334.","chicago":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” Latin American Journal of Probability and Mathematical Statistics. Instituto Nacional de Matematica Pura e Aplicada, 2018. https://doi.org/10.30757/ALEA.v15-49.","ama":"Nejjar P. Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. 2018;15(2):1311-1334. doi:10.30757/ALEA.v15-49","apa":"Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v15-49","short":"P. Nejjar, Latin American Journal of Probability and Mathematical Statistics 15 (2018) 1311–1334.","ieee":"P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,” Latin American Journal of Probability and Mathematical Statistics, vol. 15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018.","mla":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” Latin American Journal of Probability and Mathematical Statistics, vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34, doi:10.30757/ALEA.v15-49."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Nejjar, Peter","last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1705.08836"],"isi":["000460475800022"]},"title":"Transition to shocks in TASEP and decoupling of last passage times","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Latin American Journal of Probability and Mathematical Statistics","page":"1311-1334","date_published":"2018-10-01T00:00:00Z","doi":"10.30757/ALEA.v15-49","date_created":"2018-12-11T11:44:28Z","quality_controlled":"1","publisher":"Instituto Nacional de Matematica Pura e Aplicada","oa":1},{"date_updated":"2023-10-10T13:28:49Z","department":[{"_id":"MaSe"}],"_id":"44","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":98,"issue":"15","oa_version":"Preprint","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Recent realization of a kinetically constrained chain of Rydberg atoms by Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation of unusual revivals in the many-body quantum dynamics. In our previous work [C. J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to the existence of “quantum scarred” eigenstates in the many-body spectrum of the experimentally realized model. Here, we present a detailed study of the eigenstate properties of the same model. We find that the majority of the eigenstates exhibit anomalous thermalization: the observable expectation values converge to their Gibbs ensemble values, but parametrically slower compared to the predictions of the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum, we identify nonergodic eigenstates that strongly violate the ETH, whose number grows polynomially with system size. Previously, the same eigenstates were identified via large overlaps with certain product states, and were used to explain the revivals observed in experiment. Here, we find that these eigenstates, in addition to highly atypical expectation values of local observables, also exhibit subthermal entanglement entropy that scales logarithmically with the system size. Moreover, we identify an additional class of quantum scarred eigenstates, and discuss their manifestations in the dynamics starting from initial product states. We use forward scattering approximation to describe the structure and physical properties of quantum scarred eigenstates. Finally, we discuss the stability of quantum scars to various perturbations. We observe that quantum scars remain robust when the introduced perturbation is compatible with the forward scattering approximation. In contrast, the perturbations which most efficiently destroy quantum scars also lead to the restoration of “canonical” thermalization."}],"month":"10","intvolume":" 98","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.10933","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations,” Physical Review B, vol. 98, no. 15. American Physical Society, 2018.","short":"C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review B 98 (2018).","ama":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 2018;98(15). doi:10.1103/PhysRevB.98.155134","apa":"Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., & Papić, Z. (2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.155134","mla":"Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical Review B, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:10.1103/PhysRevB.98.155134.","ista":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 98(15), 155134.","chicago":"Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.155134."},"title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations","publist_id":"8010","author":[{"first_name":"C J","last_name":"Turner","full_name":"Turner, C J"},{"last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abanin, D A","last_name":"Abanin","first_name":"D A"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"first_name":"Z","last_name":"Papić","full_name":"Papić, Z"}],"article_processing_charge":"No","external_id":{"isi":["000447919100001"],"arxiv":["1806.10933"]},"article_number":"155134","day":"22","publication":"Physical Review B","isi":1,"year":"2018","doi":"10.1103/PhysRevB.98.155134","date_published":"2018-10-22T00:00:00Z","date_created":"2018-12-11T11:44:19Z","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"publication":"Physical Review Letters","day":"19","year":"2018","isi":1,"date_created":"2018-12-11T11:45:51Z","doi":"10.1103/PhysRevLett.120.124501","date_published":"2018-03-19T00:00:00Z","acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Choueiri, George H, Jose M Lopez Alonso, and Björn Hof. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.124501.","ista":"Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 120(12), 124501.","mla":"Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters, vol. 120, no. 12, 124501, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.124501.","apa":"Choueiri, G. H., Lopez Alonso, J. M., & Hof, B. (2018). Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.124501","ama":"Choueiri GH, Lopez Alonso JM, Hof B. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 2018;120(12). doi:10.1103/PhysRevLett.120.124501","ieee":"G. H. Choueiri, J. M. Lopez Alonso, and B. Hof, “Exceeding the asymptotic limit of polymer drag reduction,” Physical Review Letters, vol. 120, no. 12. American Physical Society, 2018.","short":"G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018)."},"title":"Exceeding the asymptotic limit of polymer drag reduction","external_id":{"isi":["000427804000005"]},"article_processing_charge":"No","publist_id":"7537","author":[{"last_name":"Choueiri","full_name":"Choueiri, George H","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"article_number":"124501","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"12","volume":120,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The drag of turbulent flows can be drastically decreased by adding small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the maximum drag reduction (MDR) asymptote; this asymptote is generally attributed to the dynamics being reduced to a marginal yet persistent state of subdued turbulent motion. Contrary to this accepted view, we show that, for an appropriate choice of parameters, polymers can reduce the drag beyond the suggested asymptotic limit, eliminating turbulence and giving way to laminar flow. At higher polymer concentrations, however, the laminar state becomes unstable, resulting in a fluctuating flow with the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic state is hence dynamically disconnected from ordinary turbulence. © 2018 American Physical Society."}],"acknowledged_ssus":[{"_id":"SSU"}],"intvolume":" 120","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.06271"}],"scopus_import":"1","date_updated":"2023-10-10T13:27:44Z","department":[{"_id":"BjHo"}],"_id":"328","status":"public","type":"journal_article"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review E","day":"13","year":"2018","isi":1,"date_created":"2018-12-11T11:44:49Z","doi":"10.1103/PhysRevE.98.023105","date_published":"2018-08-13T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical Society, 2018, doi:10.1103/PhysRevE.98.023105.","apa":"Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 2018;98(2). doi:10.1103/PhysRevE.98.023105","ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical Review E, vol. 98, no. 2. American Physical Society, 2018.","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018)."},"title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","external_id":{"isi":["000441466800010"],"arxiv":["1808.02088"]},"article_processing_charge":"No","author":[{"full_name":"Suri, Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra"},{"last_name":"Tithof","full_name":"Tithof, Jeffrey","first_name":"Jeffrey"},{"first_name":"Roman","full_name":"Grigoriev, Roman","last_name":"Grigoriev"},{"full_name":"Schatz, Michael","last_name":"Schatz","first_name":"Michael"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space."}],"intvolume":" 98","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":98,"issue":"2","_id":"136","status":"public","type":"journal_article","date_updated":"2023-10-10T13:29:10Z","department":[{"_id":"BjHo"}]},{"publisher":"BMJ Publishing Group","quality_controlled":"1","oa":1,"doi":"10.1136/jmedgenet-2017-104627","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:57Z","page":"48 - 54","day":"01","publication":"Journal of Medical Genetics","isi":1,"year":"2018","project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"}],"title":"A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features","author":[{"full_name":"Marin Valencia, Isaac","last_name":"Marin Valencia","first_name":"Isaac"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"first_name":"Başak","last_name":"Rosti","full_name":"Rosti, Başak"},{"first_name":"Mahmoud","full_name":"Issa, Mahmoud","last_name":"Issa"},{"first_name":"Damir","full_name":"Musaev, Damir","last_name":"Musaev"},{"first_name":"Gifty","full_name":"Bhat, Gifty","last_name":"Bhat"},{"first_name":"Eric","full_name":"Scott, Eric","last_name":"Scott"},{"last_name":"Silhavy","full_name":"Silhavy, Jennifer","first_name":"Jennifer"},{"full_name":"Stanley, Valentina","last_name":"Stanley","first_name":"Valentina"},{"last_name":"Rosti","full_name":"Rosti, Rasim","first_name":"Rasim"},{"full_name":"Gleeson, Jeremy","last_name":"Gleeson","first_name":"Jeremy"},{"last_name":"Imam","full_name":"Imam, Farhad","first_name":"Farhad"},{"full_name":"Zaki, Maha","last_name":"Zaki","first_name":"Maha"},{"last_name":"Gleeson","full_name":"Gleeson, Joseph","first_name":"Joseph"}],"publist_id":"7016","article_processing_charge":"No","external_id":{"pmid":["28626029"],"isi":["000418199800007"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev, D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627","ama":"Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54. doi:10.1136/jmedgenet-2017-104627","ieee":"I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ Publishing Group, pp. 48–54, 2018.","short":"I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev, G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki, J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.","mla":"Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.","ista":"Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 55(1), 48–54.","chicago":"Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group, 2018. https://doi.org/10.1136/jmedgenet-2017-104627."},"month":"01","intvolume":" 55","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Background: Transport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective: We aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods: Linkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function.","lang":"eng"}],"issue":"1","volume":55,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-2593"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"691","department":[{"_id":"GaNo"}],"date_updated":"2023-10-16T09:55:43Z"},{"ec_funded":1,"issue":"1-2","volume":84,"publication_status":"published","publication_identifier":{"eissn":["2064-8316"],"issn":["0001-6969"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.03305"}],"scopus_import":"1","intvolume":" 84","month":"06","abstract":[{"lang":"eng","text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere."}],"oa_version":"Preprint","department":[{"_id":"LaEr"}],"date_updated":"2023-10-16T10:29:22Z","type":"journal_article","article_type":"original","status":"public","_id":"284","page":"65 - 80","date_created":"2018-12-11T11:45:36Z","doi":"10.14232/actasm-018-753-y","date_published":"2018-06-04T00:00:00Z","year":"2018","publication":"Acta Scientiarum Mathematicarum","day":"04","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","external_id":{"arxiv":["1802.03305"]},"article_processing_charge":"No","author":[{"full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","last_name":"Virosztek","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7615","title":"Maps on probability measures preserving certain distances - a survey and some new results","citation":{"mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:10.14232/actasm-018-753-y.","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 2018;84(1-2):65-80. doi:10.14232/actasm-018-753-y","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. Springer Nature. https://doi.org/10.14232/actasm-018-753-y","ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018.","short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.","chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum. Springer Nature, 2018. https://doi.org/10.14232/actasm-018-753-y.","ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}]},{"scopus_import":"1","month":"07","intvolume":" 5","abstract":[{"lang":"eng","text":"In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density."}],"oa_version":"Published Version","volume":5,"license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"publication_identifier":{"issn":["2429-7100"],"eissn":["2270-518X"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"1ba7cccdf3900f42c4f715ae75d6813c","file_id":"5726","creator":"dernst","file_size":843938,"date_updated":"2020-07-14T12:45:16Z","file_name":"2018_JournaldeLecoleMath_Lewi.pdf","date_created":"2018-12-17T16:38:18Z"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"status":"public","_id":"180","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:45:16Z","date_updated":"2023-10-17T08:05:28Z","ddc":["510"],"quality_controlled":"1","publisher":"Ecole Polytechnique","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged.","page":"79 - 116","doi":"10.5802/jep.64","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:45:03Z","has_accepted_license":"1","year":"2018","day":"01","publication":"Journal de l'Ecole Polytechnique - Mathematiques","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"first_name":"Mathieu","last_name":"Lewi","full_name":"Lewi, Mathieu"},{"first_name":"Élliott","full_name":"Lieb, Élliott","last_name":"Lieb"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7741","external_id":{"arxiv":["1705.10676"]},"article_processing_charge":"No","title":"Statistical mechanics of the uniform electron gas","citation":{"mla":"Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5, Ecole Polytechnique, 2018, pp. 79–116, doi:10.5802/jep.64.","ieee":"M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform electron gas,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5. Ecole Polytechnique, pp. 79–116, 2018.","short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116.","apa":"Lewi, M., Lieb, É., & Seiringer, R. (2018). Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.64","ama":"Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 2018;5:79-116. doi:10.5802/jep.64","chicago":"Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2018. https://doi.org/10.5802/jep.64.","ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE Publications. https://doi.org/10.1369/0022155418786698","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","ieee":"S. Reipert et al., “Agitation modules: Flexible means to accelerate automated freeze substitution,” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Reipert, Siegfried","last_name":"Reipert","first_name":"Siegfried"},{"last_name":"Goldammer","full_name":"Goldammer, Helmuth","first_name":"Helmuth"},{"last_name":"Richardson","full_name":"Richardson, Christine","first_name":"Christine"},{"first_name":"Martin","last_name":"Goldberg","full_name":"Goldberg, Martin"},{"last_name":"Hawkins","full_name":"Hawkins, Timothy","first_name":"Timothy"},{"full_name":"Hollergschwandtner, Elena","last_name":"Hollergschwandtner","first_name":"Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"last_name":"Antreich","full_name":"Antreich, Sebastian","first_name":"Sebastian"},{"last_name":"Stierhof","full_name":"Stierhof, York","first_name":"York"}],"article_processing_charge":"No","external_id":{"pmid":["29969056"],"isi":["000452277700005"]},"title":"Agitation modules: Flexible means to accelerate automated freeze substitution","publisher":"SAGE Publications","quality_controlled":"1","oa":1,"isi":1,"year":"2018","day":"01","publication":"Journal of Histochemistry and Cytochemistry","page":"903-921","date_published":"2018-12-01T00:00:00Z","doi":"10.1369/0022155418786698","date_created":"2018-12-11T11:44:57Z","_id":"163","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-10-17T08:42:24Z","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"abstract":[{"text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1369/0022155418786698"}],"month":"12","intvolume":" 66","publication_identifier":{"issn":["0022-1554"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":66,"issue":"12"},{"date_updated":"2023-10-17T09:50:53Z","department":[{"_id":"ChLa"}],"_id":"6012","status":"public","type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10","end_date":"2018-07-15","location":"Stockholm, Sweden"},"language":[{"iso":"eng"}],"publication_status":"published","volume":80,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release"}]},"ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task.","lang":"eng"}],"month":"02","intvolume":" 80","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.07259"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations for Extrapolation and Control.” In Proceedings of the 35th International Conference on Machine Learning, 80:4442–50. ML Research Press, 2018.","ista":"Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation and control. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 4442–4450.","mla":"Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 4442–50.","apa":"Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for extrapolation and control. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research Press.","ama":"Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:4442-4450.","ieee":"S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation and control,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.","short":"S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450."},"title":"Learning equations for extrapolation and control","author":[{"full_name":"Sahoo, Subham","last_name":"Sahoo","first_name":"Subham"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1806.07259"],"isi":["000683379204058"]},"article_processing_charge":"No","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"day":"01","publication":"Proceedings of the 35th International Conference on Machine Learning","isi":1,"year":"2018","date_published":"2018-02-01T00:00:00Z","date_created":"2019-02-14T15:21:07Z","page":"4442-4450","publisher":"ML Research Press","quality_controlled":"1","oa":1},{"isi":1,"year":"2018","day":"01","publication":"Proceedings of the 35 th International Conference on Machine Learning","page":"2815-2824","date_published":"2018-02-01T00:00:00Z","date_created":"2019-02-14T14:51:57Z","publisher":"ML Research Press","quality_controlled":"1","oa":1,"citation":{"chicago":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” In Proceedings of the 35 Th International Conference on Machine Learning, 80:2815–24. ML Research Press, 2018.","ista":"Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient descent. Proceedings of the 35 th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 2815–2824.","mla":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” Proceedings of the 35 Th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.","ieee":"I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient descent,” in Proceedings of the 35 th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","ama":"Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent. In: Proceedings of the 35 Th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:2815-2824.","apa":"Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic gradient descent. In Proceedings of the 35 th International Conference on Machine Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kuzborskij, Ilja","last_name":"Kuzborskij","first_name":"Ilja"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"external_id":{"arxiv":["1703.01678"],"isi":["000683379202095"]},"article_processing_charge":"No","title":"Data-dependent stability of stochastic gradient descent","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":80,"ec_funded":1,"abstract":[{"text":"We establish a data-dependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distribution-free algorithmic stability results for SGD which depend on the worst-case constants. By virtue of the data-dependent argument, our bounds provide new insights into learning with SGD on convex and non-convex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the non-convex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. ","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01678"}],"month":"02","intvolume":" 80","date_updated":"2023-10-17T09:51:13Z","department":[{"_id":"ChLa"}],"_id":"6011","type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2018-07-15","location":"Stockholm, Sweden","start_date":"2018-07-10"},"status":"public"},{"ddc":["020"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T11:33:57Z","citation":{"mla":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors. 2018, doi:10.5281/zenodo.1244154.","apa":"Danowski, P. (2018). An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. https://doi.org/10.5281/zenodo.1244154","ama":"Danowski P. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.; 2018. doi:10.5281/zenodo.1244154","short":"P. Danowski, An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018.","ieee":"P. Danowski, An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. 2018.","chicago":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018. https://doi.org/10.5281/zenodo.1244154.","ista":"Danowski P. 2018. An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors, 5p."},"file_date_updated":"2020-07-14T12:47:10Z","title":"An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors","department":[{"_id":"E-Lib"}],"article_processing_charge":"No","author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","last_name":"Danowski"}],"_id":"5686","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":"working_paper","language":[{"iso":"eng"}],"day":"09","file":[{"date_updated":"2020-07-14T12:47:10Z","file_size":202798,"creator":"dernst","date_created":"2019-01-22T09:06:51Z","file_name":"2018_WorkingPaper_Danowski.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6cb95f8772491d155ce77c6160655fff","file_id":"5872"}],"publication_status":"published","year":"2018","has_accepted_license":"1","date_created":"2018-12-17T10:28:26Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"6657"}]},"doi":"10.5281/zenodo.1244154","date_published":"2018-05-09T00:00:00Z","page":"5","oa_version":"Published Version","month":"05","oa":1,"scopus_import":1},{"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"title":"The convergence of sparsified gradient methods","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"first_name":"Mikael","full_name":"Johansson, Mikael","last_name":"Johansson"},{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarit","full_name":"Khirirat, Sarit","last_name":"Khirirat"},{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"}],"article_processing_charge":"No","external_id":{"isi":["000461852000047"],"arxiv":["1809.10505"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983.","chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018.","short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in Advances in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: Advances in Neural Information Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., & Renggli, C. (2018). The convergence of sparsified gradient methods. In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” Advances in Neural Information Processing Systems 31, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83."},"publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","oa":1,"date_published":"2018-12-01T00:00:00Z","date_created":"2019-06-27T09:32:55Z","page":"5973-5983","day":"01","publication":"Advances in Neural Information Processing Systems 31","isi":1,"year":"2018","status":"public","type":"conference","conference":{"location":"Montreal, Canada","end_date":"2018-12-08","start_date":"2018-12-02","name":"NeurIPS: Conference on Neural Information Processing Systems"},"_id":"6589","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"date_updated":"2023-10-17T11:47:20Z","month":"12","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.10505"}],"oa_version":"Preprint","abstract":[{"text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics.","lang":"eng"}],"volume":"Volume 2018","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"_id":"7","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-10-17T11:50:05Z","department":[{"_id":"SyCr"}],"oa_version":"Published Version","abstract":[{"text":"Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups.","lang":"eng"}],"month":"11","intvolume":" 362","scopus_import":"1","main_file_link":[{"url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1095-9203"]},"publication_status":"published","issue":"6417","volume":362,"related_material":{"record":[{"status":"public","id":"13055","relation":"research_data"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/","relation":"press_release"}]},"ec_funded":1,"project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect. Science. 362(6417), 941–945.","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect,” Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science 362 (2018) 941–945.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Science. AAAS. https://doi.org/10.1126/science.aat4793","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. Science. 2018;362(6417):941-945. doi:10.1126/science.aat4793","mla":"Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45, doi:10.1126/science.aat4793."},"title":"Social network plasticity decreases disease transmission in a eusocial insect","author":[{"last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse"},{"first_name":"Alessandro","last_name":"Crespi","full_name":"Crespi, Alessandro"},{"first_name":"Danielle","full_name":"Mersch, Danielle","last_name":"Mersch"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Keller, Laurent","last_name":"Keller","first_name":"Laurent"}],"publist_id":"8049","article_processing_charge":"No","external_id":{"isi":["000451124500041"]},"acknowledgement":"This project was funded by two European Research Council Advanced Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research Council Starting Grant (SocialVaccines, 243071) to S.C.","quality_controlled":"1","publisher":"AAAS","oa":1,"day":"23","publication":"Science","isi":1,"year":"2018","doi":"10.1126/science.aat4793","date_published":"2018-11-23T00:00:00Z","date_created":"2018-12-11T11:44:07Z","page":"941 - 945"},{"publisher":"Oxford University Press","quality_controlled":"1","oa":1,"day":"28","publication":"Molecular Biology and Evolution","isi":1,"year":"2018","date_published":"2018-08-28T00:00:00Z","doi":"10.1093/molbev/msy163","date_created":"2018-12-11T11:44:11Z","page":"2669 - 2684","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","apa":"Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy163","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684."},"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","author":[{"last_name":"Palmer","full_name":"Palmer, Adam","first_name":"Adam"},{"full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"publist_id":"8036","external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"article_processing_charge":"No","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses."}],"month":"08","intvolume":" 35","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"]},"publication_status":"published","volume":35,"issue":"11","_id":"19","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-10-17T11:51:06Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"_id":"6","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T11:49:25Z","citation":{"mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments, vol. 141, MyJove Corporation, 2018, doi:10.3791/58585.","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for characterising lesions and locating electrodes in small animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation, 2018.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal of Visualized Experiments 141 (2018).","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of Visualized Experiments. MyJove Corporation. https://doi.org/10.3791/58585","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 2018;141. doi:10.3791/58585","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments. MyJove Corporation, 2018. https://doi.org/10.3791/58585.","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 141."},"department":[{"_id":"MaJö"}],"title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","external_id":{"isi":["000456469400103"]},"article_processing_charge":"No","publist_id":"8050","author":[{"last_name":"Masís","full_name":"Masís, Javier","first_name":"Javier"},{"full_name":"Mankus, David","last_name":"Mankus","first_name":"David"},{"first_name":"Steffen","full_name":"Wolff, Steffen","last_name":"Wolff"},{"first_name":"Grigori","last_name":"Guitchounts","full_name":"Guitchounts, Grigori"},{"last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Cox, David","last_name":"Cox"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies."}],"intvolume":" 141","month":"11","scopus_import":"1","quality_controlled":"1","publisher":"MyJove Corporation","publication":"Journal of visualized experiments","language":[{"iso":"eng"}],"day":"08","publication_status":"published","year":"2018","isi":1,"date_created":"2018-12-11T11:44:07Z","doi":"10.3791/58585","volume":141,"date_published":"2018-11-08T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-10-17T11:50:04Z","citation":{"chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, 10.5281/ZENODO.1322669.","mla":"Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669"},"title":"Social network plasticity decreases disease transmission in a eusocial insect","department":[{"_id":"SyCr"}],"author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"full_name":"Crespi, Alessandro","last_name":"Crespi","first_name":"Alessandro"},{"full_name":"Mersch, Danielle","last_name":"Mersch","first_name":"Danielle"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"},{"first_name":"Laurent","last_name":"Keller","full_name":"Keller, Laurent"}],"article_processing_charge":"No","_id":"13055","status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"23","year":"2018","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7"}]},"date_published":"2018-10-23T00:00:00Z","doi":"10.5281/ZENODO.1322669","date_created":"2023-05-23T13:24:51Z","oa_version":"Published Version","abstract":[{"text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n - correction of URLs within README.txt file\r\n","lang":"eng"}],"month":"10","publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"oa":1},{"publication_status":"published","publication_identifier":{"issn":["23342536"]},"language":[{"iso":"eng"}],"issue":"10","volume":5,"abstract":[{"text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"scopus_import":"1","intvolume":" 5","month":"10","date_updated":"2023-10-17T12:12:40Z","department":[{"_id":"JoFi"}],"_id":"22","type":"journal_article","article_type":"original","status":"public","year":"2018","isi":1,"publication":"Optica","day":"20","page":"1210 - 1219","date_created":"2018-12-11T11:44:12Z","doi":"10.1364/OPTICA.5.001210","date_published":"2018-10-20T00:00:00Z","oa":1,"quality_controlled":"1","citation":{"mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10, 2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210.","ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210","apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210","ieee":"G. Botello et al., “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” Optica, vol. 5, no. 10. pp. 1210–1219, 2018.","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219.","chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, 2018. https://doi.org/10.1364/OPTICA.5.001210.","ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000447853100007"]},"article_processing_charge":"No","publist_id":"8033","author":[{"full_name":"Botello, Gabriel","last_name":"Botello","first_name":"Gabriel"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez"},{"first_name":"Kerlos","last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos"},{"last_name":"Brown","full_name":"Brown, Elliott","first_name":"Elliott"},{"first_name":"Gerd","full_name":"Leuchs, Gerd","last_name":"Leuchs"},{"last_name":"Preu","full_name":"Preu, Sascha","first_name":"Sascha"},{"last_name":"Segovia Vargas","full_name":"Segovia Vargas, Daniel","first_name":"Daniel"},{"last_name":"Strekalov","full_name":"Strekalov, Dmitry","first_name":"Dmitry"},{"full_name":"Munoz, Luis","last_name":"Munoz","first_name":"Luis"},{"full_name":"Schwefel, Harald","last_name":"Schwefel","first_name":"Harald"}],"title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters"},{"title":"Contracts for system design","author":[{"first_name":"Albert","last_name":"Benveniste","full_name":"Benveniste, Albert"},{"first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"full_name":"Caillaud, Benoît","last_name":"Caillaud","first_name":"Benoît"},{"last_name":"Passerone","full_name":"Passerone, Roberto","first_name":"Roberto"},{"full_name":"Raclet, Jean Baptiste","last_name":"Raclet","first_name":"Jean Baptiste"},{"last_name":"Reinkemeier","full_name":"Reinkemeier, Philipp","first_name":"Philipp"},{"first_name":"Alberto","full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni-Vincentelli"},{"first_name":"Werner","last_name":"Damm","full_name":"Damm, Werner"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Kim G.","last_name":"Larsen","full_name":"Larsen, Kim G."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053.","ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","mla":"Benveniste, Albert, et al. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:10.1561/1000000053.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","ieee":"A. Benveniste et al., “Contracts for system design,” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053"},"publisher":"Now Publishers","quality_controlled":"1","oa":1,"date_published":"2018-05-01T00:00:00Z","doi":"10.1561/1000000053","date_created":"2018-12-16T22:59:19Z","page":"124-400","day":"01","publication":"Foundations and Trends in Electronic Design Automation","year":"2018","status":"public","type":"journal_article","article_type":"original","_id":"5677","department":[{"_id":"ToHe"}],"date_updated":"2023-10-17T11:53:09Z","month":"05","intvolume":" 12","scopus_import":"1","main_file_link":[{"url":"https://hal.inria.fr/hal-00757488/","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector."}],"issue":"2-3","volume":12,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1551-3939"]},"publication_status":"published"}]