[{"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1117"},{"id":"749","status":"public","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"date_updated":"2023-09-27T12:26:03Z","title":"Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release","month":"03","date_published":"2018-03-01T00:00:00Z","article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:04Z","pubrep_id":"997","supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"page":"110","_id":"324","date_created":"2018-12-11T11:45:49Z","publication_status":"published","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."}],"publist_id":"7541","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:04Z","file_size":8719458,"relation":"main_file","checksum":"8e163ae9e927401b9fa7c1b3e6a3631a","access_level":"open_access","file_name":"IST-2018-997-v1+1_Thesis_chong_a.pdf","file_id":"5046","date_created":"2018-12-12T10:13:58Z","creator":"system"},{"date_created":"2019-04-05T09:25:26Z","creator":"dernst","file_id":"6221","access_level":"closed","file_name":"2018_Thesis_chong_source.pages","date_updated":"2020-07-14T12:46:04Z","content_type":"application/octet-stream","file_size":47841940,"relation":"source_file","checksum":"f7d7260029a5fbb5c982db61328ade52"}],"type":"dissertation","citation":{"ama":"Chen C. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. 2018. doi:10.15479/AT:ISTA:th_997","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.","ista":"Chen C. 2018. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria.","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.","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","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."},"ddc":["571"],"degree_awarded":"PhD","department":[{"_id":"PeJo"}],"publication_identifier":{"issn":["2663-337X"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chong"}],"year":"2018","doi":"10.15479/AT:ISTA:th_997","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","day":"01"},{"date_published":"2018-01-01T00:00:00Z","date_updated":"2021-01-12T07:42:07Z","title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","month":"01","_id":"325","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"date_created":"2018-12-11T11:45:50Z","external_id":{"arxiv":["1709.04037"]},"article_number":"34","issue":"POPL","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":" 2","volume":2,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"author":[{"first_name":"Sheshansh","last_name":"Agrawal","full_name":"Agrawal, Sheshansh"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novotny","full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"}],"year":"2018","conference":{"start_date":"2018-01-07","location":"Los Angeles, CA, USA","end_date":"2018-01-13","name":"POPL: Principles of Programming Languages"},"department":[{"_id":"KrCh"}],"publisher":"ACM","day":"01","doi":"10.1145/3158122","arxiv":1,"oa_version":"Preprint","quality_controlled":"1","abstract":[{"text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach.","lang":"eng"}],"publication_status":"published","publist_id":"7540","language":[{"iso":"eng"}],"status":"public","type":"conference","citation":{"ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.","apa":"Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","mla":"Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122.","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122."}},{"ddc":["570"],"acknowledged_ssus":[{"_id":"EM-Fac"}],"file":[{"file_id":"5721","creator":"dernst","date_created":"2018-12-17T16:16:50Z","relation":"main_file","checksum":"98e901d8229e44aa8f3b51d248dedd09","file_size":4850261,"date_updated":"2020-07-14T12:46:06Z","content_type":"application/pdf","file_name":"2018_EJN_Sawada.pdf","access_level":"open_access"}],"citation":{"ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901.","ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901.","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","apa":"Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901"},"type":"journal_article","quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites."}],"publist_id":"7539","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publisher":"Wiley","day":"07","doi":"10.1111/ejn.13901","oa_version":"Published Version","author":[{"first_name":"Kazuaki","last_name":"Sawada","full_name":"Sawada, Kazuaki"},{"last_name":"Kawakami","full_name":"Kawakami, Ryosuke","first_name":"Ryosuke"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Tomomi","last_name":"Nemoto","full_name":"Nemoto, Tomomi"}],"isi":1,"year":"2018","department":[{"_id":"RySh"}],"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"9","oa":1,"intvolume":" 47","volume":47,"_id":"326","date_created":"2018-12-11T11:45:50Z","external_id":{"isi":["000431496400001"]},"file_date_updated":"2020-07-14T12:46:06Z","publication":"European Journal of Neuroscience","page":"1033 - 1042","date_published":"2018-03-07T00:00:00Z","article_processing_charge":"No","title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","date_updated":"2023-09-19T09:58:40Z","month":"03"},{"date_updated":"2023-09-18T09:31:46Z","title":"Slow dynamics in translation-invariant quantum lattice models","month":"03","article_processing_charge":"No","date_published":"2018-03-19T00:00:00Z","publication":"Physical Review B","_id":"327","external_id":{"isi":["000427798800005"]},"date_created":"2018-12-11T11:45:50Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"volume":97,"article_number":"104307","intvolume":" 97","oa":1,"issue":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","scopus_import":"1","department":[{"_id":"MaSe"}],"year":"2018","author":[{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marko","last_name":"Žnidarič","full_name":"Žnidarič, Marko"},{"full_name":"Medvedyeva, Mariya","last_name":"Medvedyeva","first_name":"Mariya"},{"last_name":"Abanin","full_name":"Abanin, Dmitry","first_name":"Dmitry"},{"full_name":"Prosen, Tomaž","last_name":"Prosen","first_name":"Tomaž"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"}],"isi":1,"doi":"10.1103/PhysRevB.97.104307","oa_version":"Preprint","publisher":"American Physical Society","day":"19","publist_id":"7538","abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307.","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018."}},{"department":[{"_id":"BjHo"}],"year":"2018","isi":1,"author":[{"full_name":"Choueiri, George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H"},{"orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"oa_version":"Preprint","doi":"10.1103/PhysRevLett.120.124501","day":"19","publisher":"American Physical Society","status":"public","language":[{"iso":"eng"}],"publist_id":"7537","publication_status":"published","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"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.","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","short":"G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018).","ista":"Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 120(12), 124501.","mla":"Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters, vol. 120, no. 12, 124501, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.124501.","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","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."},"acknowledged_ssus":[{"_id":"SSU"}],"month":"03","date_updated":"2023-10-10T13:27:44Z","title":"Exceeding the asymptotic limit of polymer drag reduction","ec_funded":1,"article_processing_charge":"No","date_published":"2018-03-19T00:00:00Z","publication":"Physical Review Letters","external_id":{"isi":["000427804000005"]},"date_created":"2018-12-11T11:45:51Z","_id":"328","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.06271"}],"volume":120,"oa":1,"intvolume":" 120","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","issue":"12","article_number":"124501","scopus_import":"1"},{"scopus_import":"1","volume":2018,"oa":1,"intvolume":" 2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","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).","article_number":"e5325","publication":"PeerJ","file_date_updated":"2020-07-14T12:46:06Z","external_id":{"pmid":["30294507"],"isi":["000447204400001"]},"date_created":"2018-12-11T11:44:16Z","_id":"33","month":"10","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","date_updated":"2023-10-17T12:24:43Z","article_processing_charge":"No","date_published":"2018-10-01T00:00:00Z","citation":{"short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","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","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.","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","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.","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."},"type":"journal_article","file":[{"creator":"dernst","date_created":"2018-12-17T10:46:06Z","file_id":"5692","file_name":"2018_PeerJ_Bertl.pdf","access_level":"open_access","checksum":"3334886c4b39678db4c4b74299ca14ba","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z","file_size":1328344}],"ddc":["576"],"status":"public","pmid":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"8022","publication_status":"published","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","oa_version":"Published Version","doi":"10.7717/peerj.5325","day":"01","publisher":"PeerJ","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"NiBa"}],"year":"2018","isi":1,"author":[{"last_name":"Bertl","full_name":"Bertl, Johanna","first_name":"Johanna"},{"full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald"},{"first_name":"Michaël","last_name":"Blum","full_name":"Blum, Michaël"}]},{"edition":"1","date_published":"2018-06-08T00:00:00Z","author":[{"last_name":"Clarke","full_name":"Clarke, Edmund M.","first_name":"Edmund M."},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"article_processing_charge":"No","year":"2018","month":"06","title":"Handbook of Model Checking","date_updated":"2025-07-24T09:25:31Z","department":[{"_id":"ToHe"}],"publication_identifier":{"isbn":["978-3-319-10574-1"],"eisbn":["978-3-319-10575-8"]},"retracted":"1","date_created":"2018-12-11T12:02:32Z","day":"08","_id":"3300","publisher":"Springer Nature","oa_version":"None","page":"XLVIII, 1212","doi":"10.1007/978-3-319-10575-8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Cham","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools.","lang":"eng"}],"publist_id":"3340","scopus_import":"1","type":"book","citation":{"ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","mla":"Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8.","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8","chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8."}},{"department":[{"_id":"KrCh"}],"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Chemlík","full_name":"Chemlík, Martin"},{"full_name":"Topcu, Ufuk","last_name":"Topcu","first_name":"Ufuk"}],"isi":1,"year":"2018","conference":{"location":"Delft, Netherlands","start_date":"2018-06-24","end_date":"2018-06-29","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"oa_version":"Preprint","arxiv":1,"publisher":"AAAI Press","day":"01","abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies.","lang":"eng"}],"publication_status":"published","publist_id":"8021","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","citation":{"ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018.","ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55.","mla":"Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55.","short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.","apa":"Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55."},"type":"conference","date_updated":"2023-09-19T14:44:14Z","title":"Sensor synthesis for POMDPs with reachability objectives","month":"06","date_published":"2018-06-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"page":"47 - 55","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"_id":"34","date_created":"2018-12-11T11:44:16Z","external_id":{"isi":["000492986200006"],"arxiv":["1710.00675"]},"volume":2018,"alternative_title":["ICAPS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.00675"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 2018","oa":1,"scopus_import":"1"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.07031","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"9293"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publication":"28th International Conference on Automated Planning and Scheduling ","date_created":"2018-12-11T11:44:17Z","external_id":{"isi":["000492986200007"],"arxiv":["1804.07031"]},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"_id":"35","month":"06","title":"Algorithms and conditional lower bounds for planning problems","date_updated":"2023-09-26T10:41:41Z","ec_funded":1,"date_published":"2018-06-01T00:00:00Z","article_processing_charge":"No","citation":{"short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2018). Algorithms and conditional lower bounds for planning problems. In 28th International Conference on Automated Planning and Scheduling . Delft, Netherlands: AAAI Press.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” in 28th International Conference on Automated Planning and Scheduling , Delft, Netherlands, 2018.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In 28th International Conference on Automated Planning and Scheduling . AAAI Press, 2018.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. In: 28th International Conference on Automated Planning and Scheduling . AAAI Press; 2018.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional lower bounds for planning problems. 28th International Conference on Automated Planning and Scheduling . ICAPS: International Conference on Automated Planning and Scheduling.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018."},"type":"conference","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"We consider planning problems for graphs, Markov decision processes (MDPs), and games on graphs. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems where there are k different target sets, and the problems are as follows: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) objective-separation results showing that for MDPs the coverage problem is harder than the sequential target problem.","lang":"eng"}],"publist_id":"8020","quality_controlled":"1","arxiv":1,"oa_version":"None","day":"01","publisher":"AAAI Press","department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Wolfgang","full_name":"Dvorák, Wolfgang","last_name":"Dvorák"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Alexander","last_name":"Svozil","full_name":"Svozil, Alexander"}],"isi":1,"conference":{"end_date":"2018-06-29","start_date":"2018-06-24","location":"Delft, Netherlands","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"year":"2018"},{"volume":69,"issue":"19","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":" 69","scopus_import":"1","month":"08","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","date_updated":"2023-09-19T10:00:46Z","date_published":"2018-08-31T00:00:00Z","article_processing_charge":"No","page":"4609 - 4624","file_date_updated":"2020-07-14T12:46:13Z","publication":"Journal of Experimental Botany","date_created":"2018-12-11T11:44:17Z","external_id":{"isi":["000443568700010"]},"_id":"36","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.","lang":"eng"}],"publication_status":"published","publist_id":"8019","quality_controlled":"1","citation":{"chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018."},"type":"journal_article","file":[{"creator":"dernst","date_created":"2018-12-18T09:47:51Z","file_id":"5741","access_level":"open_access","file_name":"2018_JournalExperimBotany_Vu.pdf","file_size":3359316,"date_updated":"2020-07-14T12:46:13Z","content_type":"application/pdf","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","relation":"main_file"}],"ddc":["581"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"JiFr"}],"isi":1,"author":[{"first_name":"Lam","full_name":"Vu, Lam","last_name":"Vu"},{"full_name":"Zhu, Tingting","last_name":"Zhu","first_name":"Tingting"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"}],"year":"2018","oa_version":"Published Version","doi":"10.1093/jxb/ery204","day":"31","publisher":"Oxford University Press"},{"oa_version":"Submitted Version","doi":"10.1007/978-1-4939-8772-6_4","day":"16","publisher":"Springer Nature","series_title":"MIMB","department":[{"_id":"AnKi"}],"publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"author":[{"last_name":"Zagórski","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"year":"2018","citation":{"ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4."},"type":"book_chapter","file":[{"success":1,"access_level":"open_access","file_name":"2018_MIMB_Zagorski.pdf","date_updated":"2020-10-13T14:20:37Z","content_type":"application/pdf","file_size":4906815,"relation":"main_file","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","creator":"dernst","date_created":"2020-10-13T14:20:37Z","file_id":"8656"}],"ddc":["570"],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube."}],"publist_id":"8018","quality_controlled":"1","page":"47 - 63","file_date_updated":"2020-10-13T14:20:37Z","publication":"Morphogen Gradients ","date_created":"2018-12-11T11:44:17Z","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"_id":"37","month":"10","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","date_updated":"2021-01-12T07:49:03Z","ec_funded":1,"date_published":"2018-10-16T00:00:00Z","article_processing_charge":"No","scopus_import":"1","volume":1863,"alternative_title":["Methods in Molecular Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":" 1863"},{"month":"10","title":"Selection and gene flow shape genomic islands that control floral guides","date_updated":"2023-09-18T08:36:49Z","article_processing_charge":"No","date_published":"2018-10-23T00:00:00Z","page":"11006 - 11011","publication":"PNAS","file_date_updated":"2020-07-14T12:46:16Z","external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"date_created":"2018-12-11T11:44:18Z","_id":"38","volume":115,"oa":1,"intvolume":" 115","acknowledgement":" ERC Grant 201252 (to N.H.B.)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"43","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["00278424"]},"department":[{"_id":"NiBa"}],"year":"2018","isi":1,"author":[{"first_name":"Hugo","last_name":"Tavares","full_name":"Tavares, Hugo"},{"first_name":"Annabel","last_name":"Whitley","full_name":"Whitley, Annabel"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"last_name":"Bradley","full_name":"Bradley, Desmond","first_name":"Desmond"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"first_name":"Joane","full_name":"Elleouet, Joane","last_name":"Elleouet"},{"last_name":"Burrus","full_name":"Burrus, Monique","first_name":"Monique"},{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"last_name":"Li","full_name":"Li, Miaomiao","first_name":"Miaomiao"},{"first_name":"Qun","last_name":"Li","full_name":"Li, Qun"},{"full_name":"Xue, Yongbiao","last_name":"Xue","first_name":"Yongbiao"},{"first_name":"Alexandra B","full_name":"Rebocho, Alexandra B","last_name":"Rebocho"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"oa_version":"Published Version","doi":"10.1073/pnas.1801832115","day":"23","publisher":"National Academy of Sciences","status":"public","pmid":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"8017","publication_status":"published","abstract":[{"lang":"eng","text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation."}],"quality_controlled":"1","type":"journal_article","citation":{"ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115"},"file":[{"file_id":"5683","date_created":"2018-12-17T08:44:03Z","creator":"dernst","file_size":1911302,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:16Z","relation":"main_file","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","access_level":"open_access","file_name":"11006.full.pdf"}],"ddc":["570"]},{"intvolume":" 10","oa":1,"acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","issue":"3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":10,"scopus_import":"1","article_processing_charge":"No","date_published":"2018-03-01T00:00:00Z","date_updated":"2023-09-11T13:56:52Z","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","month":"03","_id":"384","external_id":{"isi":["000429483700022"]},"date_created":"2018-12-11T11:46:10Z","publication":"Genome Biology and Evolution","file_date_updated":"2020-07-14T12:46:16Z","pubrep_id":"999","page":"928 - 938","quality_controlled":"1","publist_id":"7445","publication_status":"published","abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"ddc":["576"],"file":[{"creator":"system","date_created":"2018-12-12T10:08:07Z","file_id":"4667","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","access_level":"open_access","checksum":"458a7c2c2e79528567edfeb0f326cbe0","relation":"main_file","date_updated":"2020-07-14T12:46:16Z","content_type":"application/pdf","file_size":691602}],"citation":{"mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938."},"type":"journal_article","year":"2018","isi":1,"author":[{"full_name":"Hönigschmid, Peter","last_name":"Hönigschmid","first_name":"Peter"},{"first_name":"Nadya","full_name":"Bykova, Nadya","last_name":"Bykova"},{"last_name":"Schneider","full_name":"Schneider, René","first_name":"René"},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"last_name":"Frishman","full_name":"Frishman, Dmitrij","first_name":"Dmitrij"}],"department":[{"_id":"FyKo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Oxford University Press","day":"01","doi":"10.1093/gbe/evy049","oa_version":"Published Version"},{"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"volume":210,"oa":1,"intvolume":" 210","issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Genetics","page":"1411-1427","_id":"39","external_id":{"isi":["000452315900021"]},"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:10:29Z","title":"Replicability of introgression under linked, polygenic selection","month":"12","article_processing_charge":"No","date_published":"2018-12-04T00:00:00Z","type":"journal_article","citation":{"ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427."},"article_type":"original","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1534/genetics.118.301429","oa_version":"Preprint","publisher":"Genetics Society of America","day":"04","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["00166731"]},"year":"2018","isi":1,"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}]},{"day":"10","publisher":"American Chemical Society","oa_version":"Submitted Version","arxiv":1,"doi":"10.1021/acs.nanolett.7b03953","author":[{"first_name":"Fahad","full_name":"Mahmood, Fahad","last_name":"Mahmood"},{"last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lee","full_name":"Lee, Yi","first_name":"Yi"},{"first_name":"Jing","full_name":"Kong, Jing","last_name":"Kong"},{"first_name":"Nuh","full_name":"Gedik, Nuh","last_name":"Gedik"}],"year":"2018","citation":{"mla":"Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters, vol. 18, no. 1, American Chemical Society, 2018, pp. 223–28, doi:10.1021/acs.nanolett.7b03953.","ista":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1), 223–228.","ama":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 2018;18(1):223-228. doi:10.1021/acs.nanolett.7b03953","chicago":"Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.7b03953.","ieee":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,” Nano Letters, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018.","short":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018) 223–228.","apa":"Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., & Gedik, N. (2018). Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b03953"},"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"The valley pseudospin in monolayer transition metal dichalcogenides (TMDs) has been proposed as a new way to manipulate information in various optoelectronic devices. This relies on a large valley polarization that remains stable over long time scales (hundreds of nanoseconds). However, time-resolved measurements report valley lifetimes of only a few picoseconds. This has been attributed to mechanisms such as phonon-mediated intervalley scattering and a precession of the valley pseudospin through electron-hole exchange. Here we use transient spin grating to directly measure the valley depolarization lifetime in monolayer MoSe2. We find a fast valley decay rate that scales linearly with the excitation density at different temperatures. This establishes the presence of strong exciton-exciton Coulomb exchange interactions enhancing the valley depolarization. Our work highlights the microscopic processes inhibiting the efficient use of the exciton valley pseudospin in monolayer TMDs. "}],"publist_id":"7435","date_created":"2018-12-11T11:46:13Z","external_id":{"arxiv":["1712.07925"]},"_id":"394","page":"223 - 228","publication":"Nano Letters","date_published":"2018-01-10T00:00:00Z","month":"01","title":"Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2","date_updated":"2021-01-12T07:53:20Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","oa":1,"intvolume":" 18","volume":18,"main_file_link":[{"url":"https://arxiv.org/abs/1712.07925","open_access":"1"}]},{"date_published":"2018-03-01T00:00:00Z","article_processing_charge":"No","title":"The branched chain amino acids in autism spectrum disorders ","date_updated":"2023-09-07T12:38:59Z","month":"03","project":[{"call_identifier":"FWF","grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease"}],"_id":"395","date_created":"2018-12-11T11:46:14Z","file_date_updated":"2021-02-11T23:30:15Z","pubrep_id":"992","supervisor":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"page":"88","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"1183","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara"}],"year":"2018","degree_awarded":"PhD","department":[{"_id":"GaNo"}],"publication_identifier":{"issn":["2663-337X"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","day":"01","doi":"10.15479/AT:ISTA:th_992","oa_version":"Published Version","abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ","lang":"eng"}],"publication_status":"published","publist_id":"7434","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","ddc":["570","616"],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"file":[{"creator":"dernst","date_created":"2019-04-05T09:19:17Z","file_id":"6217","access_level":"closed","embargo_to":"open_access","file_name":"2018_Thesis_Tarlungeanu_source.docx","date_updated":"2021-02-11T23:30:15Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":43684035,"checksum":"9f5231c96e0ad945040841a8630232da","relation":"source_file"},{"access_level":"open_access","file_name":"2018_Thesis_Tarlungeanu.pdf","file_size":30511532,"date_updated":"2021-02-11T11:17:16Z","content_type":"application/pdf","checksum":"0c33c370aa2010df5c552db57a6d01e9","relation":"main_file","date_created":"2019-04-05T09:19:17Z","creator":"dernst","embargo":"2018-03-15","file_id":"6218"}],"citation":{"ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","mla":"Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992.","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992","chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","apa":"Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018."},"type":"dissertation"},{"date_updated":"2023-09-11T14:10:25Z","title":"Harnessing epoch-based reclamation for efficient range queries","month":"02","article_processing_charge":"No","date_published":"2018-02-10T00:00:00Z","page":"14 - 27","_id":"397","external_id":{"isi":["000446161100002"]},"date_created":"2018-12-11T11:46:14Z","volume":53,"alternative_title":["PPoPP"],"intvolume":" 53","issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"department":[{"_id":"DaAl"}],"year":"2018","conference":{"name":"PPoPP: Principles and Practice of Parallel Programming","start_date":"2018-02-24","location":"Vienna, Austria","end_date":"2018-02-28"},"author":[{"first_name":"Maya","full_name":"Arbel Raviv, Maya","last_name":"Arbel Raviv"},{"last_name":"Brown","full_name":"Brown, Trevor A","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"doi":"10.1145/3178487.3178489","oa_version":"None","publisher":"ACM","day":"10","publist_id":"7430","publication_status":"published","abstract":[{"text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. ","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","citation":{"ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","mla":"Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489.","ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489","chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.","ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.","apa":"Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489"}},{"publication_status":"published","abstract":[{"lang":"eng","text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices."}],"volume":13,"publist_id":"7431","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 13","type":"journal_article","citation":{"ieee":"P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096","short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.","mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.","ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578.","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096","chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096."},"scopus_import":"1","date_updated":"2023-09-11T14:12:33Z","title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","department":[{"_id":"BeBi"}],"month":"05","author":[{"full_name":"Dodier, Philippe","last_name":"Dodier","first_name":"Philippe"},{"first_name":"Josa","full_name":"Frischer, Josa","last_name":"Frischer"},{"first_name":"Wei","full_name":"Wang, Wei","last_name":"Wang"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Ammar","last_name":"Mallouhi","full_name":"Mallouhi, Ammar"},{"first_name":"Wolfgang","full_name":"Serles, Wolfgang","last_name":"Serles"},{"full_name":"Gruber, Andreas","last_name":"Gruber","first_name":"Andreas"},{"last_name":"Knosp","full_name":"Knosp, Engelbert","first_name":"Engelbert"},{"last_name":"Bavinzski","full_name":"Bavinzski, Gerhard","first_name":"Gerhard"}],"isi":1,"date_published":"2018-05-01T00:00:00Z","article_processing_charge":"No","year":"2018","doi":"10.1016/j.wneu.2018.02.096","publication":"World Neurosurgery","oa_version":"None","page":"e568-e578","_id":"398","publisher":"Elsevier","date_created":"2018-12-11T11:46:15Z","external_id":{"isi":["000432942700070"]},"day":"01"},{"date_published":"2018-01-01T00:00:00Z","article_processing_charge":"No","month":"01","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","date_updated":"2023-09-08T13:30:51Z","date_created":"2018-12-11T11:46:15Z","external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"399","publication":"EPL","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","oa":1,"intvolume":" 121","article_number":"10007","volume":121,"main_file_link":[{"url":"https://arxiv.org/abs/1706.01822","open_access":"1"}],"scopus_import":"1","isi":1,"author":[{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reuvers, Robin","last_name":"Reuvers","first_name":"Robin"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"year":"2018","department":[{"_id":"RoSe"}],"day":"01","publisher":"IOP Publishing Ltd.","oa_version":"Preprint","arxiv":1,"doi":"10.1209/0295-5075/121/10007","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm."}],"publist_id":"7432","article_type":"original","type":"journal_article","citation":{"ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007.","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007."}},{"scopus_import":"1","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","relation":"press_release"}]},"volume":37,"intvolume":" 37","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","article_number":"89","publication":"ACM Trans. Graph.","file_date_updated":"2020-07-14T12:46:22Z","pubrep_id":"1049","external_id":{"isi":["000448185000050"]},"date_created":"2018-12-11T11:44:06Z","_id":"4","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020"}],"month":"08","title":"Learning three-dimensional flow for interactive aerodynamic design","date_updated":"2023-09-13T08:46:15Z","ec_funded":1,"article_processing_charge":"No","date_published":"2018-08-04T00:00:00Z","type":"journal_article","citation":{"apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89."},"file":[{"file_size":22803163,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:22Z","relation":"main_file","checksum":"7a2243668f215821bc6aecad0320079a","access_level":"open_access","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","file_id":"5216","date_created":"2018-12-12T10:16:28Z","creator":"system"}],"ddc":["003","004"],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"8053","abstract":[{"lang":"eng","text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body."}],"publication_status":"published","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1145/3197517.3201325","day":"04","publisher":"ACM","department":[{"_id":"BeBi"}],"year":"2018","author":[{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"isi":1}]