[{"file":[{"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","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5046","checksum":"8e163ae9e927401b9fa7c1b3e6a3631a"},{"file_size":47841940,"date_updated":"2020-07-14T12:46:04Z","creator":"dernst","file_name":"2018_Thesis_chong_source.pages","date_created":"2019-04-05T09:25:26Z","content_type":"application/octet-stream","relation":"source_file","access_level":"closed","checksum":"f7d7260029a5fbb5c982db61328ade52","file_id":"6221"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"1117","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"749"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"03","alternative_title":["ISTA Thesis"],"ddc":["571"],"supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"date_updated":"2023-09-27T12:26:03Z","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:46:04Z","_id":"324","status":"public","pubrep_id":"997","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)"},"day":"01","has_accepted_license":"1","year":"2018","date_published":"2018-03-01T00:00:00Z","doi":"10.15479/AT:ISTA:th_997","date_created":"2018-12-11T11:45:49Z","page":"110","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"C. Chen, Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release, Institute of Science and Technology Austria, 2018.","ieee":"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.","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."},"title":"Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release","publist_id":"7541","author":[{"id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong","last_name":"Chen","full_name":"Chen, Chong"}],"article_processing_charge":"No"},{"date_updated":"2023-09-27T12:29:57Z","ddc":["514","516"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:58Z","_id":"742","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","pubrep_id":"912","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5835","checksum":"d2f70fc132156504aa4c626aa378a7ab","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"s10711-017-0291-4.pdf","date_created":"2019-01-15T13:44:05Z","creator":"kschuh","file_size":412486,"date_updated":"2020-07-14T12:47:58Z"}],"volume":195,"related_material":{"record":[{"relation":"earlier_version","id":"1378","status":"public"}]},"issue":"1","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 195","month":"08","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.","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","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","ieee":"D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” Geometriae Dedicata, vol. 195, no. 1. Springer, pp. 307–317, 2018.","short":"D. Dotterrer, T. Kaufman, U. Wagner, Geometriae Dedicata 195 (2018) 307–317.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000437122700017"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"6925","author":[{"full_name":"Dotterrer, Dominic","last_name":"Dotterrer","first_name":"Dominic"},{"first_name":"Tali","full_name":"Kaufman, Tali","last_name":"Kaufman"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"title":"On expansion and topological overlap","project":[{"grant_number":"PP00P2_138948","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","_id":"25FA3206-B435-11E9-9278-68D0E5697425"}],"year":"2018","isi":1,"has_accepted_license":"1","publication":"Geometriae Dedicata","day":"01","page":"307–317","date_created":"2018-12-11T11:48:16Z","doi":"10.1007/s10711-017-0291-4","date_published":"2018-08-01T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1"},{"author":[{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Nejjar, Peter","last_name":"Nejjar"}],"external_id":{"isi":["000460475800022"],"arxiv":["1705.08836"]},"article_processing_charge":"No","title":"Transition to shocks in TASEP and decoupling of last passage times","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.","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.","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","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","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"1311-1334","doi":"10.30757/ALEA.v15-49","date_published":"2018-10-01T00:00:00Z","date_created":"2018-12-11T11:44:28Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Latin American Journal of Probability and Mathematical Statistics","publisher":"Instituto Nacional de Matematica Pura e Aplicada","quality_controlled":"1","oa":1,"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:46Z","date_updated":"2023-10-10T13:11:29Z","ddc":["510"],"article_type":"original","type":"journal_article","status":"public","_id":"70","issue":"2","volume":15,"ec_funded":1,"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"}],"scopus_import":"1","month":"10","intvolume":" 15","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version"},{"month":"10","intvolume":" 98","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10933"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"volume":98,"issue":"15","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"44","department":[{"_id":"MaSe"}],"date_updated":"2023-10-10T13:28:49Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"doi":"10.1103/PhysRevB.98.155134","date_published":"2018-10-22T00:00:00Z","date_created":"2018-12-11T11:44:19Z","day":"22","publication":"Physical Review B","isi":1,"year":"2018","article_number":"155134","title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations","author":[{"first_name":"C J","full_name":"Turner, C J","last_name":"Turner"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Abanin","full_name":"Abanin, D A","first_name":"D A"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Papić","full_name":"Papić, Z","first_name":"Z"}],"publist_id":"8010","external_id":{"arxiv":["1806.10933"],"isi":["000447919100001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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"}},{"status":"public","type":"journal_article","_id":"328","department":[{"_id":"BjHo"}],"date_updated":"2023-10-10T13:27:44Z","intvolume":" 120","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.06271"}],"scopus_import":"1","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"}],"ec_funded":1,"issue":"12","volume":120,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"124501","title":"Exceeding the asymptotic limit of polymer drag reduction","article_processing_charge":"No","external_id":{"isi":["000427804000005"]},"publist_id":"7537","author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H","last_name":"Choueiri","full_name":"Choueiri, George H"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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).","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."},"oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","date_created":"2018-12-11T11:45:51Z","date_published":"2018-03-19T00:00:00Z","doi":"10.1103/PhysRevLett.120.124501","publication":"Physical Review Letters","day":"19","year":"2018","isi":1},{"citation":{"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.","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","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","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","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.","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)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1808.02088"],"isi":["000441466800010"]},"article_processing_charge":"No","author":[{"id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra","full_name":"Suri, Balachandra","last_name":"Suri"},{"first_name":"Jeffrey","last_name":"Tithof","full_name":"Tithof, Jeffrey"},{"first_name":"Roman","last_name":"Grigoriev","full_name":"Grigoriev, Roman"},{"first_name":"Michael","last_name":"Schatz","full_name":"Schatz, Michael"}],"title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","year":"2018","isi":1,"publication":"Physical Review E","day":"13","date_created":"2018-12-11T11:44:49Z","date_published":"2018-08-13T00:00:00Z","doi":"10.1103/PhysRevE.98.023105","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2023-10-10T13:29:10Z","department":[{"_id":"BjHo"}],"_id":"136","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":98,"issue":"2","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"scopus_import":"1","intvolume":" 98","month":"08"},{"project":[{"name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299","_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","article_processing_charge":"No","external_id":{"isi":["000418199800007"],"pmid":["28626029"]},"author":[{"full_name":"Marin Valencia, Isaac","last_name":"Marin Valencia","first_name":"Isaac"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johansen","full_name":"Johansen, Anide","first_name":"Anide"},{"last_name":"Rosti","full_name":"Rosti, Başak","first_name":"Başak"},{"first_name":"Mahmoud","last_name":"Issa","full_name":"Issa, Mahmoud"},{"first_name":"Damir","last_name":"Musaev","full_name":"Musaev, Damir"},{"full_name":"Bhat, Gifty","last_name":"Bhat","first_name":"Gifty"},{"first_name":"Eric","full_name":"Scott, Eric","last_name":"Scott"},{"full_name":"Silhavy, Jennifer","last_name":"Silhavy","first_name":"Jennifer"},{"last_name":"Stanley","full_name":"Stanley, Valentina","first_name":"Valentina"},{"first_name":"Rasim","full_name":"Rosti, Rasim","last_name":"Rosti"},{"first_name":"Jeremy","last_name":"Gleeson","full_name":"Gleeson, Jeremy"},{"full_name":"Imam, Farhad","last_name":"Imam","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","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.","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."},"oa":1,"publisher":"BMJ Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:47:57Z","doi":"10.1136/jmedgenet-2017-104627","date_published":"2018-01-01T00:00:00Z","page":"48 - 54","publication":"Journal of Medical Genetics","day":"01","year":"2018","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"691","department":[{"_id":"GaNo"}],"date_updated":"2023-10-16T09:55:43Z","intvolume":" 55","month":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/"}],"scopus_import":"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"}],"volume":55,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-2593"]}},{"publist_id":"7615","author":[{"full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","last_name":"Virosztek","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1802.03305"]},"article_processing_charge":"No","title":"Maps on probability measures preserving certain distances - a survey and some new results","citation":{"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.","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.","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","short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"65 - 80","date_published":"2018-06-04T00:00:00Z","doi":"10.14232/actasm-018-753-y","date_created":"2018-12-11T11:45:36Z","year":"2018","day":"04","publication":"Acta Scientiarum Mathematicarum","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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).","department":[{"_id":"LaEr"}],"date_updated":"2023-10-16T10:29:22Z","type":"journal_article","article_type":"original","status":"public","_id":"284","issue":"1-2","volume":84,"ec_funded":1,"publication_identifier":{"eissn":["2064-8316"],"issn":["0001-6969"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.03305"}],"month":"06","intvolume":" 84","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint"},{"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"title":"Statistical mechanics of the uniform electron gas","author":[{"first_name":"Mathieu","last_name":"Lewi","full_name":"Lewi, Mathieu"},{"last_name":"Lieb","full_name":"Lieb, Élliott","first_name":"Élliott"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"7741","article_processing_charge":"No","external_id":{"arxiv":["1705.10676"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116.","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.","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","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.","ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.","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."},"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.","doi":"10.5802/jep.64","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:45:03Z","page":"79 - 116","day":"01","publication":"Journal de l'Ecole Polytechnique - Mathematiques","has_accepted_license":"1","year":"2018","status":"public","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)"},"_id":"180","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:45:16Z","ddc":["510"],"date_updated":"2023-10-17T08:05:28Z","month":"07","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":5,"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5726","checksum":"1ba7cccdf3900f42c4f715ae75d6813c","creator":"dernst","date_updated":"2020-07-14T12:45:16Z","file_size":843938,"date_created":"2018-12-17T16:38:18Z","file_name":"2018_JournaldeLecoleMath_Lewi.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"publication_status":"published"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-1554"]},"publication_status":"published","volume":66,"issue":"12","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"12","intvolume":" 66","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1369/0022155418786698","open_access":"1"}],"date_updated":"2023-10-17T08:42:24Z","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"_id":"163","status":"public","article_type":"original","type":"journal_article","day":"01","publication":"Journal of Histochemistry and Cytochemistry","isi":1,"year":"2018","doi":"10.1369/0022155418786698","date_published":"2018-12-01T00:00:00Z","date_created":"2018-12-11T11:44:57Z","page":"903-921","quality_controlled":"1","publisher":"SAGE Publications","oa":1,"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.","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.","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.","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","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","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."},"title":"Agitation modules: Flexible means to accelerate automated freeze substitution","author":[{"last_name":"Reipert","full_name":"Reipert, Siegfried","first_name":"Siegfried"},{"full_name":"Goldammer, Helmuth","last_name":"Goldammer","first_name":"Helmuth"},{"full_name":"Richardson, Christine","last_name":"Richardson","first_name":"Christine"},{"last_name":"Goldberg","full_name":"Goldberg, Martin","first_name":"Martin"},{"first_name":"Timothy","full_name":"Hawkins, Timothy","last_name":"Hawkins"},{"id":"3C054040-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Hollergschwandtner","full_name":"Hollergschwandtner, Elena"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"last_name":"Antreich","full_name":"Antreich, Sebastian","first_name":"Sebastian"},{"first_name":"York","last_name":"Stierhof","full_name":"Stierhof, York"}],"external_id":{"pmid":["29969056"],"isi":["000452277700005"]},"article_processing_charge":"No"},{"_id":"6012","type":"conference","conference":{"location":"Stockholm, Sweden","end_date":"2018-07-15","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning"},"status":"public","date_updated":"2023-10-17T09:50:53Z","department":[{"_id":"ChLa"}],"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"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.07259","open_access":"1"}],"month":"02","intvolume":" 80","publication_status":"published","language":[{"iso":"eng"}],"volume":80,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release","description":"News on IST Homepage"}]},"ec_funded":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Sahoo","full_name":"Sahoo, Subham","first_name":"Subham"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"}],"article_processing_charge":"No","external_id":{"isi":["000683379204058"],"arxiv":["1806.07259"]},"title":"Learning equations for extrapolation and control","quality_controlled":"1","publisher":"ML Research Press","oa":1,"isi":1,"year":"2018","day":"01","publication":"Proceedings of the 35th International Conference on Machine Learning","page":"4442-4450","date_published":"2018-02-01T00:00:00Z","date_created":"2019-02-14T15:21:07Z"},{"status":"public","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10","location":"Stockholm, Sweden","end_date":"2018-07-15"},"type":"conference","_id":"6011","department":[{"_id":"ChLa"}],"date_updated":"2023-10-17T09:51:13Z","intvolume":" 80","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1703.01678","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","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"}],"ec_funded":1,"volume":80,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"title":"Data-dependent stability of stochastic gradient descent","article_processing_charge":"No","external_id":{"arxiv":["1703.01678"],"isi":["000683379202095"]},"author":[{"full_name":"Kuzborskij, Ilja","last_name":"Kuzborskij","first_name":"Ilja"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","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.","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.","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.","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."},"oa":1,"quality_controlled":"1","publisher":"ML Research Press","date_created":"2019-02-14T14:51:57Z","date_published":"2018-02-01T00:00:00Z","page":"2815-2824","publication":"Proceedings of the 35 th International Conference on Machine Learning","day":"01","year":"2018","isi":1},{"_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","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"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","ieee":"P. Danowski, An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. 2018.","short":"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."},"date_updated":"2023-10-17T11:33:57Z","title":"An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors","file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"E-Lib"}],"article_processing_charge":"No","author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","last_name":"Danowski","orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick"}],"oa_version":"Published Version","month":"05","oa":1,"scopus_import":1,"language":[{"iso":"eng"}],"day":"09","file":[{"file_id":"5872","checksum":"6cb95f8772491d155ce77c6160655fff","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-01-22T09:06:51Z","file_name":"2018_WorkingPaper_Danowski.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:10Z","file_size":202798}],"publication_status":"published","year":"2018","has_accepted_license":"1","date_created":"2018-12-17T10:28:26Z","doi":"10.5281/zenodo.1244154","related_material":{"record":[{"relation":"later_version","status":"public","id":"6657"}]},"date_published":"2018-05-09T00:00:00Z","page":"5"},{"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"}],"month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.10505"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":"Volume 2018","_id":"6589","status":"public","conference":{"start_date":"2018-12-02","location":"Montreal, Canada","end_date":"2018-12-08","name":"NeurIPS: Conference on Neural Information Processing Systems"},"type":"conference","date_updated":"2023-10-17T11:47:20Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"oa":1,"publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","publication":"Advances in Neural Information Processing Systems 31","day":"01","year":"2018","isi":1,"date_created":"2019-06-27T09:32:55Z","date_published":"2018-12-01T00:00:00Z","page":"5973-5983","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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.","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.","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."},"title":"The convergence of sparsified gradient methods","article_processing_charge":"No","external_id":{"isi":["000461852000047"],"arxiv":["1809.10505"]},"author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"},{"first_name":"Mikael","last_name":"Johansson","full_name":"Johansson, Mikael"},{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H"},{"full_name":"Khirirat, Sarit","last_name":"Khirirat","first_name":"Sarit"},{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"}]},{"date_created":"2018-12-11T11:44:07Z","date_published":"2018-11-23T00:00:00Z","doi":"10.1126/science.aat4793","page":"941 - 945","publication":"Science","day":"23","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"AAAS","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.","title":"Social network plasticity decreases disease transmission in a eusocial insect","article_processing_charge":"No","external_id":{"isi":["000451124500041"]},"publist_id":"8049","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"},{"last_name":"Crespi","full_name":"Crespi, Alessandro","first_name":"Alessandro"},{"first_name":"Danielle","last_name":"Mersch","full_name":"Mersch, Danielle"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"full_name":"Keller, Laurent","last_name":"Keller","first_name":"Laurent"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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.","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."},"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ec_funded":1,"issue":"6417","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/","relation":"press_release"}],"record":[{"relation":"research_data","id":"13055","status":"public"}]},"volume":362,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1095-9203"]},"intvolume":" 362","month":"11","main_file_link":[{"open_access":"1","url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"department":[{"_id":"SyCr"}],"date_updated":"2023-10-17T11:50:05Z","status":"public","type":"journal_article","article_type":"original","_id":"7"},{"day":"28","publication":"Molecular Biology and Evolution","isi":1,"year":"2018","doi":"10.1093/molbev/msy163","date_published":"2018-08-28T00:00:00Z","date_created":"2018-12-11T11:44:11Z","page":"2669 - 2684","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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."},"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","publist_id":"8036","author":[{"first_name":"Adam","full_name":"Palmer, Adam","last_name":"Palmer"},{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"]},"publication_status":"published","volume":35,"issue":"11","oa_version":"Submitted Version","pmid":1,"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":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"date_updated":"2023-10-17T11:51:06Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"19","status":"public","type":"journal_article","article_type":"original"},{"type":"journal_article","status":"public","_id":"6","article_processing_charge":"No","external_id":{"isi":["000456469400103"]},"publist_id":"8050","author":[{"full_name":"Masís, Javier","last_name":"Masís","first_name":"Javier"},{"first_name":"David","full_name":"Mankus, David","last_name":"Mankus"},{"full_name":"Wolff, Steffen","last_name":"Wolff","first_name":"Steffen"},{"full_name":"Guitchounts, Grigori","last_name":"Guitchounts","first_name":"Grigori"},{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cox, David","last_name":"Cox","first_name":"David"}],"department":[{"_id":"MaJö"}],"title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","date_updated":"2023-10-17T11:49:25Z","citation":{"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.","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"MyJove Corporation","scopus_import":"1","intvolume":" 141","month":"11","abstract":[{"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.","lang":"eng"}],"oa_version":"None","date_created":"2018-12-11T11:44:07Z","doi":"10.3791/58585","volume":141,"date_published":"2018-11-08T00:00:00Z","publication_status":"published","year":"2018","isi":1,"publication":"Journal of visualized experiments","language":[{"iso":"eng"}],"day":"08"},{"_id":"13055","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)"},"status":"public","date_updated":"2023-10-17T11:50:04Z","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, Zenodo, 10.5281/ZENODO.1322669.","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.","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","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","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.","mla":"Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Crespi","full_name":"Crespi, Alessandro","first_name":"Alessandro"},{"full_name":"Mersch, Danielle","last_name":"Mersch","first_name":"Danielle"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Keller","full_name":"Keller, Laurent","first_name":"Laurent"}],"article_processing_charge":"No","title":"Social network plasticity decreases disease transmission in a eusocial insect","department":[{"_id":"SyCr"}],"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"}],"oa_version":"Published Version","publisher":"Zenodo","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.1480665"}],"month":"10","year":"2018","day":"23","related_material":{"record":[{"relation":"used_in_publication","id":"7","status":"public"}]},"date_published":"2018-10-23T00:00:00Z","doi":"10.5281/ZENODO.1322669","date_created":"2023-05-23T13:24:51Z"},{"type":"journal_article","article_type":"original","status":"public","_id":"22","department":[{"_id":"JoFi"}],"date_updated":"2023-10-17T12:12:40Z","scopus_import":"1","main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"month":"10","intvolume":" 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","issue":"10","volume":5,"publication_identifier":{"issn":["23342536"]},"publication_status":"published","language":[{"iso":"eng"}],"publist_id":"8033","author":[{"first_name":"Gabriel","full_name":"Botello, Gabriel","last_name":"Botello"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kerlos","last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos"},{"first_name":"Elliott","last_name":"Brown","full_name":"Brown, Elliott"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Sascha","last_name":"Preu","full_name":"Preu, Sascha"},{"first_name":"Daniel","last_name":"Segovia Vargas","full_name":"Segovia Vargas, Daniel"},{"first_name":"Dmitry","last_name":"Strekalov","full_name":"Strekalov, Dmitry"},{"last_name":"Munoz","full_name":"Munoz, Luis","first_name":"Luis"},{"first_name":"Harald","full_name":"Schwefel, Harald","last_name":"Schwefel"}],"external_id":{"isi":["000447853100007"]},"article_processing_charge":"No","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","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.","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.","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","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","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","quality_controlled":"1","oa":1,"page":"1210 - 1219","date_published":"2018-10-20T00:00:00Z","doi":"10.1364/OPTICA.5.001210","date_created":"2018-12-11T11:44:12Z","isi":1,"year":"2018","day":"20","publication":"Optica"},{"intvolume":" 12","month":"05","main_file_link":[{"url":"https://hal.inria.fr/hal-00757488/","open_access":"1"}],"scopus_import":"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."}],"volume":12,"issue":"2-3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1551-3939"]},"status":"public","type":"journal_article","article_type":"original","_id":"5677","department":[{"_id":"ToHe"}],"date_updated":"2023-10-17T11:53:09Z","oa":1,"quality_controlled":"1","publisher":"Now Publishers","date_created":"2018-12-16T22:59:19Z","doi":"10.1561/1000000053","date_published":"2018-05-01T00:00:00Z","page":"124-400","publication":"Foundations and Trends in Electronic Design Automation","day":"01","year":"2018","title":"Contracts for system design","article_processing_charge":"No","author":[{"last_name":"Benveniste","full_name":"Benveniste, Albert","first_name":"Albert"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"},{"first_name":"Benoît","last_name":"Caillaud","full_name":"Caillaud, Benoît"},{"first_name":"Roberto","full_name":"Passerone, Roberto","last_name":"Passerone"},{"last_name":"Raclet","full_name":"Raclet, Jean Baptiste","first_name":"Jean Baptiste"},{"first_name":"Philipp","last_name":"Reinkemeier","full_name":"Reinkemeier, Philipp"},{"first_name":"Alberto","last_name":"Sangiovanni-Vincentelli","full_name":"Sangiovanni-Vincentelli, Alberto"},{"full_name":"Damm, Werner","last_name":"Damm","first_name":"Werner"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Larsen","full_name":"Larsen, Kim G.","first_name":"Kim G."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","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."}},{"oa_version":"Preprint","abstract":[{"text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum.","lang":"eng"}],"month":"02","intvolume":" 43","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1711.01986","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":43,"ec_funded":1,"_id":"435","status":"public","type":"journal_article","date_updated":"2023-10-17T12:15:06Z","department":[{"_id":"MiLe"}],"acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","publisher":"Optica Publishing Group","quality_controlled":"1","oa":1,"day":"01","publication":"Optics Letters","isi":1,"year":"2018","date_published":"2018-02-01T00:00:00Z","doi":"10.1364/OL.43.000607","date_created":"2018-12-11T11:46:27Z","page":"607 - 610","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing Group, 2018. https://doi.org/10.1364/OL.43.000607.","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607","apa":"Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.43.000607","ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018.","short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607."},"title":"Coherent-perfect-absorber and laser for bound states in a continuum","author":[{"first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali","last_name":"Midya"},{"full_name":"Konotop, Vladimir","last_name":"Konotop","first_name":"Vladimir"}],"publist_id":"7388","external_id":{"isi":["000423776600066"],"arxiv":["1711.01986"]},"article_processing_charge":"No"},{"article_number":"30083438","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","external_id":{"isi":["000440484800002"]},"article_processing_charge":"No","author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"full_name":"Gagnaire, Pierre","last_name":"Gagnaire","first_name":"Pierre"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"last_name":"Faivre","full_name":"Faivre, Nicolas","first_name":"Nicolas"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"publist_id":"7784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438."},"oa":1,"quality_controlled":"1","publisher":"PeerJ","date_created":"2018-12-11T11:44:50Z","date_published":"2018-07-30T00:00:00Z","doi":"10.7717/peerj.5198","publication":"PeerJ","day":"30","year":"2018","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","_id":"139","file_date_updated":"2020-07-14T12:44:48Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-10-17T12:25:28Z","intvolume":" 2018","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"volume":2018,"issue":"7","language":[{"iso":"eng"}],"file":[{"file_id":"5739","checksum":"7d55ae22598a1c70759cd671600cff53","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-18T09:42:11Z","file_name":"2018_PeerJ_Fraisse.pdf","date_updated":"2020-07-14T12:44:48Z","file_size":1480792,"creator":"dernst"}],"publication_status":"published"},{"publication":"PeerJ","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:16Z","doi":"10.7717/peerj.5325","date_published":"2018-10-01T00:00:00Z","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","oa":1,"quality_controlled":"1","publisher":"PeerJ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325.","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325."},"title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","article_processing_charge":"No","external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"publist_id":"8022","author":[{"last_name":"Bertl","full_name":"Bertl, Johanna","first_name":"Johanna"},{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682"},{"last_name":"Blum","full_name":"Blum, Michaël","first_name":"Michaël"}],"article_number":"e5325","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1328344,"date_updated":"2020-07-14T12:46:06Z","file_name":"2018_PeerJ_Bertl.pdf","date_created":"2018-12-17T10:46:06Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5692","checksum":"3334886c4b39678db4c4b74299ca14ba"}],"publication_status":"published","volume":2018,"issue":"10","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.","lang":"eng"}],"intvolume":" 2018","month":"10","scopus_import":"1","ddc":["576"],"date_updated":"2023-10-17T12:24:43Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:06Z","_id":"33","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"},{"date_updated":"2023-10-17T12:19:28Z","department":[{"_id":"JiFr"}],"_id":"5673","type":"journal_article","status":"public","publication_identifier":{"issn":["2055-0278"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"12","volume":4,"ec_funded":1,"abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833","open_access":"1"}],"month":"12","intvolume":" 4","citation":{"mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"external_id":{"pmid":["30518833"],"isi":["000454576600017"]},"article_processing_charge":"No","title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"isi":1,"year":"2018","day":"03","publication":"Nature Plants","page":"1082-1088","date_published":"2018-12-03T00:00:00Z","doi":"10.1038/s41477-018-0318-3","date_created":"2018-12-16T22:59:18Z","quality_controlled":"1","publisher":"Nature Research","oa":1},{"title":"Language acquisition with communication between learners","external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"article_processing_charge":"No","author":[{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"publist_id":"7715","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073.","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:10.1098/rsif.2018.0073.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language acquisition with communication between learners. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. Journal of the Royal Society Interface. 2018;15(140). doi:10.1098/rsif.2018.0073","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” Journal of the Royal Society Interface, vol. 15, no. 140. The Royal Society, 2018.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018)."},"project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"20180073","date_created":"2018-12-11T11:45:09Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1098/rsif.2018.0073","publication":"Journal of the Royal Society Interface","day":"01","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"The Royal Society","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-10-18T06:36:00Z","status":"public","article_type":"original","type":"journal_article","_id":"198","ec_funded":1,"issue":"140","volume":15,"related_material":{"record":[{"status":"public","id":"9814","relation":"research_data"}],"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971","relation":"supplementary_material"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"5955","checksum":"444e1a9d98eb0e780671be82b13025f3","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_RS_IbsenJensen.pdf","date_created":"2019-02-12T07:54:37Z","file_size":219837,"date_updated":"2020-07-14T12:45:22Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1742-5662"]},"intvolume":" 15","month":"03","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students.","lang":"eng"}]},{"_id":"5859","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":"2023-10-18T06:41:12Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:47:13Z","abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 5","month":"12","publication_status":"published","publication_identifier":{"issn":["2054-5703"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:13Z","file_size":646732,"creator":"dernst","date_created":"2019-02-05T14:38:09Z","file_name":"2018_RoyalSocOS_Corominas.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5924","checksum":"9664d4417f6b792242e31eea77ce9501"}],"volume":5,"issue":"12","article_number":"181286","citation":{"chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000456566500027"],"pmid":["30662738"]},"author":[{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fibla","full_name":"Fibla, Martí Sànchez","first_name":"Martí Sànchez"},{"full_name":"Valverde, Sergi","last_name":"Valverde","first_name":"Sergi"},{"last_name":"Solé","full_name":"Solé, Ricard","first_name":"Ricard"}],"title":"Chromatic transitions in the emergence of syntax networks","acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","oa":1,"publisher":"The Royal Society","quality_controlled":"1","year":"2018","isi":1,"has_accepted_license":"1","publication":"Royal Society Open Science","day":"12","date_created":"2019-01-20T22:59:18Z","doi":"10.1098/rsos.181286","date_published":"2018-12-12T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-18T10:46:08Z","citation":{"chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752.","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. .","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv."},"department":[{"_id":"LaEr"}],"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Alt, Johannes","last_name":"Alt"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.07752"]},"article_number":"1804.07752","_id":"6183","status":"public","type":"preprint","day":"20","language":[{"iso":"eng"}],"publication":"arXiv","year":"2018","publication_status":"submitted","related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"},{"id":"14694","status":"public","relation":"later_version"}]},"date_published":"2018-04-20T00:00:00Z","date_created":"2019-03-28T09:20:06Z","oa_version":"Preprint","abstract":[{"text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases.","lang":"eng"}],"month":"04","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07752"}]},{"month":"09","publisher":"arXiv","main_file_link":[{"url":"https://arxiv.org/abs/1804.03057","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higher-dimensional generalization."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8156"}]},"date_published":"2018-09-13T00:00:00Z","doi":"10.48550/arXiv.1804.03057","date_created":"2018-12-11T11:44:30Z","ec_funded":1,"day":"13","language":[{"iso":"eng"}],"year":"2018","publication_status":"published","status":"public","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"type":"preprint","article_number":"1804.03057","_id":"75","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"title":"Convex fair partitions into arbitrary number of pieces","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"last_name":"Karasev","full_name":"Karasev, Roman","first_name":"Roman"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.03057"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.","ieee":"A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary number of pieces.” arXiv, 2018.","short":"A. Akopyan, S. Avvakumov, R. Karasev, (2018).","apa":"Akopyan, A., Avvakumov, S., & Karasev, R. (2018). Convex fair partitions into arbitrary number of pieces. arXiv. https://doi.org/10.48550/arXiv.1804.03057","ama":"Akopyan A, Avvakumov S, Karasev R. Convex fair partitions into arbitrary number of pieces. 2018. doi:10.48550/arXiv.1804.03057","chicago":"Akopyan, Arseniy, Sergey Avvakumov, and Roman Karasev. “Convex Fair Partitions into Arbitrary Number of Pieces.” arXiv, 2018. https://doi.org/10.48550/arXiv.1804.03057.","ista":"Akopyan A, Avvakumov S, Karasev R. 2018. Convex fair partitions into arbitrary number of pieces. 1804.03057."},"date_updated":"2023-12-18T10:51:02Z"},{"_id":"556","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":"2024-02-20T10:48:17Z","ddc":["500"],"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"lang":"eng","text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"11","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0c38abe73569b7166b7487ad5d23cc68","file_id":"5866","date_updated":"2020-07-14T12:47:03Z","file_size":3084674,"creator":"dernst","date_created":"2019-01-21T15:18:55Z","file_name":"2018_Annales_Betea.pdf"}],"ec_funded":1,"volume":19,"issue":"12","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1.","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary Schur process and applications I. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-018-0723-1","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.","ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. 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The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:53Z","department":[{"_id":"GaTk"}],"date_updated":"2024-02-21T13:45:25Z","ddc":["570"],"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":"292"},{"project":[{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931.","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., & Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 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Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079."},"title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000429009500021"]},"author":[{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller"},{"first_name":"Alexandra","full_name":"Vandervelde, Alexandra","last_name":"Vandervelde"},{"first_name":"Tanino","last_name":"Albanese","full_name":"Albanese, Tanino"},{"first_name":"Lendert","last_name":"Gelens","full_name":"Gelens, Lendert"},{"first_name":"Isabella","last_name":"Moll","full_name":"Moll, Isabella"}],"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","publication":"Nucleic Acids Research","day":"06","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:46:29Z","doi":"10.1093/nar/gky079","date_published":"2018-04-06T00:00:00Z","page":"2918-2931","_id":"438","pubrep_id":"971","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","ddc":["576"],"date_updated":"2024-02-21T13:44:45Z","file_date_updated":"2020-07-14T12:46:27Z","department":[{"_id":"CaGu"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress."}],"intvolume":" 46","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"5151","checksum":"3ff4f545c27e11a4cd20ccb30778793e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","date_created":"2018-12-12T10:15:30Z","file_size":5027978,"date_updated":"2020-07-14T12:46:27Z","creator":"system"}],"publication_status":"published","related_material":{"record":[{"relation":"popular_science","id":"5569","status":"public"}]},"volume":46,"issue":"6"},{"ddc":["570"],"date_updated":"2024-02-21T13:45:12Z","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:44:43Z","_id":"131","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","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":3158125,"date_updated":"2020-07-14T12:44:43Z","file_name":"2018_eLife_Picard.pdf","date_created":"2018-12-17T11:55:05Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5695","checksum":"d6331d4385b1fffd6b47b45d5949d841"}],"publication_status":"published","volume":7,"related_material":{"record":[{"status":"public","id":"5586","relation":"popular_science"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"intvolume":" 7","month":"08","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684.","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684.","ieee":"M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684"},"title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","external_id":{"isi":["000441388200001"]},"article_processing_charge":"No","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","last_name":"Picard","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A"},{"first_name":"Celine","full_name":"Cosseau, Celine","last_name":"Cosseau"},{"first_name":"Sabrina","full_name":"Ferré, Sabrina","last_name":"Ferré"},{"full_name":"Quack, Thomas","last_name":"Quack","first_name":"Thomas"},{"first_name":"Christoph","last_name":"Grevelding","full_name":"Grevelding, Christoph"},{"first_name":"Yohann","full_name":"Couté, Yohann","last_name":"Couté"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7792","article_number":"e35684","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"publication":"eLife","day":"13","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:47Z","doi":"10.7554/eLife.35684","date_published":"2018-08-13T00:00:00Z","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications"},{"month":"03","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. "}],"related_material":{"record":[{"id":"292","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:98","date_published":"2018-03-29T00:00:00Z","date_created":"2018-12-12T12:31:39Z","day":"29","file":[{"file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","date_created":"2018-12-12T13:02:24Z","creator":"system","file_size":1142543971,"date_updated":"2020-07-14T12:47:07Z","file_id":"5590","checksum":"6808748837b9afbbbabc2a356ca2b88a","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5591","checksum":"d6d6cd07743038fe3a12352983fcf9dd","creator":"system","file_size":702336,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","date_created":"2018-12-12T13:02:25Z"},{"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","file_id":"5592","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","date_updated":"2020-07-14T12:47:07Z","file_size":432,"creator":"system","date_created":"2018-12-12T13:02:26Z","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat"},{"checksum":"2a83b011012e21e934b4596285b1a183","file_id":"5593","access_level":"open_access","relation":"main_file","content_type":"text/plain","date_created":"2018-12-12T13:02:26Z","file_name":"IST-2018-98-v1+4_README.txt","creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":986}],"has_accepted_license":"1","year":"2018","datarep_id":"98","project":[{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26"}],"status":"public","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5584","file_date_updated":"2020-07-14T12:47:07Z","title":"Nonlinear decoding of a complex movie from the mammalian retina","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"author":[{"last_name":"Deny","full_name":"Deny, Stephane","first_name":"Stephane"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"full_name":"Botella-Soler, Vicente","last_name":"Botella-Soler","first_name":"Vicente"},{"first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","last_name":"Martius"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-02-21T13:45:26Z","citation":{"ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98.","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98."}},{"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"citation":{"ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000441753000007"]},"article_processing_charge":"No","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","acknowledgement":"ERC, Grant/Award Number: 250152","publisher":"Wiley","quality_controlled":"1","year":"2018","isi":1,"publication":"Molecular Ecology Resources","day":"01","page":"988 - 999","date_created":"2018-12-11T11:45:37Z","date_published":"2018-09-01T00:00:00Z","doi":"10.1111/1755-0998.12782","_id":"286","type":"journal_article","status":"public","date_updated":"2024-02-21T13:45:00Z","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. "}],"oa_version":"None","scopus_import":"1","intvolume":" 18","month":"09","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"id":"5583","status":"public","relation":"popular_science"}]},"issue":"5","volume":18},{"month":"07","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)."}],"date_published":"2018-07-24T00:00:00Z","related_material":{"record":[{"relation":"research_paper","id":"131","status":"public"}]},"doi":"10.15479/AT:ISTA:109","date_created":"2018-12-12T12:31:40Z","contributor":[{"orcid":"0000-0002-8101-2518","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A"}],"file":[{"checksum":"e60b484bd6f55c08eb66a189cb72c923","file_id":"5601","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","date_created":"2018-12-12T13:02:35Z","creator":"system","file_size":11918144,"date_updated":"2020-07-14T12:47:08Z"}],"day":"24","has_accepted_license":"1","datarep_id":"109","year":"2018","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"status":"public","keyword":["schistosoma","Z-chromosome","gene expression"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5586","file_date_updated":"2020-07-14T12:47:08Z","department":[{"_id":"BeVi"}],"title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","author":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","short":"B. Vicoso, (2018).","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109","mla":"Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109.","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109."},"date_updated":"2024-02-21T13:45:12Z"},{"has_accepted_license":"1","year":"2018","datarep_id":"95","file":[{"date_created":"2018-12-12T13:02:41Z","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","date_updated":"2020-07-14T12:47:07Z","file_size":122048,"creator":"system","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_id":"5606","content_type":"text/csv","access_level":"open_access","relation":"main_file"},{"file_size":235980,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","date_created":"2018-12-12T13:02:42Z","content_type":"text/csv","relation":"main_file","access_level":"open_access","file_id":"5607","checksum":"92347586ae4f8a6eb7c04354797bf314"},{"date_created":"2018-12-12T13:02:43Z","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","date_updated":"2020-07-14T12:47:07Z","file_size":311712,"creator":"system","checksum":"3300813645a54e6c5c39f41917228354","file_id":"5608","content_type":"text/csv","access_level":"open_access","relation":"main_file"},{"file_size":342090,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_created":"2018-12-12T13:02:44Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_id":"5609","checksum":"e739fc473567fd8f39438b445fc46147"}],"day":"12","date_published":"2018-02-12T00:00:00Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"286"}]},"doi":"10.15479/AT:ISTA:95","date_created":"2018-12-12T12:31:39Z","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","date_updated":"2024-02-21T13:45:01Z","citation":{"mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","short":"T. Ellis, (2018).","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254"}],"article_processing_charge":"No","title":"Data and Python scripts supporting Python package FAPS","file_date_updated":"2020-07-14T12:47:07Z","department":[{"_id":"NiBa"}],"_id":"5583","type":"research_data","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)"},"status":"public"},{"oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","abstract":[{"text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic.","lang":"eng"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:35Z","doi":"10.15479/AT:ISTA:74","date_published":"2018-02-07T00:00:00Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"438"}]},"year":"2018","datarep_id":"74","has_accepted_license":"1","file":[{"creator":"system","file_size":3558703796,"date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","date_created":"2018-12-12T13:04:39Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5637","checksum":"61ebb92213cfffeba3ddbaff984b81af"},{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5638","checksum":"bf26649af310ef6892d68576515cde6d","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":1830422606,"date_created":"2018-12-12T13:04:55Z","file_name":"IST-2018-74-v1+3_15-07-31.zip"},{"date_created":"2018-12-12T13:05:11Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":2140849248,"file_id":"5639","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"day":"07","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","keyword":["microscopy","microfluidics"],"status":"public","_id":"5569","article_processing_charge":"No","author":[{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"}],"publist_id":"7385","file_date_updated":"2020-07-14T12:47:04Z","title":"Time-lapse microscopy data","department":[{"_id":"CaGu"}],"date_updated":"2024-02-21T13:44:45Z","citation":{"chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","short":"T. Bergmiller, N. Nikolic, (2018)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["579"]},{"author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"},{"first_name":"Andersson Anna","last_name":"Mc","full_name":"Mc, Andersson Anna"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publist_id":"7760","article_processing_charge":"No","external_id":{"isi":["000440149300021"]},"title":"Statistical mechanics for metabolic networks during steady state growth","citation":{"ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"2988","date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41467-018-05417-9","date_created":"2018-12-11T11:44:57Z","has_accepted_license":"1","isi":1,"year":"2018","day":"30","publication":"Nature Communications","publisher":"Springer Nature","quality_controlled":"1","oa":1,"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:06Z","date_updated":"2024-02-21T13:45:39Z","ddc":["570"],"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":"161","related_material":{"record":[{"id":"5587","status":"public","relation":"popular_science"}]},"volume":9,"issue":"1","ec_funded":1,"publication_status":"published","file":[{"file_id":"5728","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_NatureComm_DeMartino.pdf","date_created":"2018-12-17T16:44:28Z","creator":"dernst","file_size":1043205,"date_updated":"2020-07-14T12:45:06Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 9","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"oa_version":"Published Version"}]