[{"month":"12","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"volume":5,"issue":"12","file":[{"file_id":"5924","checksum":"9664d4417f6b792242e31eea77ce9501","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_RoyalSocOS_Corominas.pdf","date_created":"2019-02-05T14:38:09Z","file_size":646732,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2054-5703"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"5859","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-10-18T06:41:12Z","quality_controlled":"1","publisher":"The Royal Society","oa":1,"acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","date_published":"2018-12-12T00:00:00Z","doi":"10.1098/rsos.181286","date_created":"2019-01-20T22:59:18Z","day":"12","publication":"Royal Society Open Science","isi":1,"has_accepted_license":"1","year":"2018","article_number":"181286","title":"Chromatic transitions in the emergence of syntax networks","author":[{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"last_name":"Fibla","full_name":"Fibla, Martí Sànchez","first_name":"Martí Sànchez"},{"first_name":"Sergi","full_name":"Valverde, Sergi","last_name":"Valverde"},{"full_name":"Solé, Ricard","last_name":"Solé","first_name":"Ricard"}],"article_processing_charge":"No","external_id":{"pmid":["30662738"],"isi":["000456566500027"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286."}},{"publication_status":"submitted","year":"2018","day":"20","language":[{"iso":"eng"}],"publication":"arXiv","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"},{"status":"public","id":"14694","relation":"later_version"}]},"date_published":"2018-04-20T00:00:00Z","date_created":"2019-03-28T09:20:06Z","abstract":[{"text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases.","lang":"eng"}],"oa_version":"Preprint","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.07752","open_access":"1"}],"month":"04","date_updated":"2023-12-18T10:46:08Z","citation":{"chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752.","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. .","apa":"Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alt","full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.07752"]},"department":[{"_id":"LaEr"}],"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","_id":"6183","article_number":"1804.07752","type":"preprint","status":"public"},{"year":"2018","publication_status":"published","day":"13","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"8156","relation":"dissertation_contains"}]},"date_published":"2018-09-13T00:00:00Z","doi":"10.48550/arXiv.1804.03057","ec_funded":1,"date_created":"2018-12-11T11:44:30Z","abstract":[{"lang":"eng","text":"We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higher-dimensional generalization."}],"oa_version":"Preprint","publisher":"arXiv","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.03057"}],"oa":1,"month":"09","date_updated":"2023-12-18T10:51:02Z","citation":{"ieee":"A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary number of pieces.” arXiv, 2018.","short":"A. Akopyan, S. Avvakumov, R. Karasev, (2018).","ama":"Akopyan A, Avvakumov S, Karasev R. Convex fair partitions into arbitrary number of pieces. 2018. doi:10.48550/arXiv.1804.03057","apa":"Akopyan, A., Avvakumov, S., & Karasev, R. (2018). Convex fair partitions into arbitrary number of pieces. arXiv. https://doi.org/10.48550/arXiv.1804.03057","mla":"Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.","ista":"Akopyan A, Avvakumov S, Karasev R. 2018. Convex fair partitions into arbitrary number of pieces. 1804.03057.","chicago":"Akopyan, Arseniy, Sergey Avvakumov, and Roman Karasev. “Convex Fair Partitions into Arbitrary Number of Pieces.” arXiv, 2018. https://doi.org/10.48550/arXiv.1804.03057."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"first_name":"Roman","last_name":"Karasev","full_name":"Karasev, Roman"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.03057"]},"title":"Convex fair partitions into arbitrary number of pieces","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"_id":"75","article_number":"1804.03057","type":"preprint","status":"public","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"publication":"Annales Henri Poincare","day":"13","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:47:09Z","doi":"10.1007/s00023-018-0723-1","date_published":"2018-11-13T00:00:00Z","page":"3663-3742","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary Schur process and applications I. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-018-0723-1","mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1."},"title":"The free boundary Schur process and applications I","external_id":{"arxiv":["1704.05809"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"7258","author":[{"first_name":"Dan","last_name":"Betea","full_name":"Betea, Dan"},{"full_name":"Bouttier, Jeremie","last_name":"Bouttier","first_name":"Jeremie"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"},{"full_name":"Vuletic, Mirjana","last_name":"Vuletic","first_name":"Mirjana"}],"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:03Z","file_size":3084674,"creator":"dernst","date_created":"2019-01-21T15:18:55Z","file_name":"2018_Annales_Betea.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5866","checksum":"0c38abe73569b7166b7487ad5d23cc68"}],"publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"ec_funded":1,"volume":19,"issue":"12","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions."}],"intvolume":" 19","month":"11","scopus_import":"1","ddc":["500"],"date_updated":"2024-02-20T10:48:17Z","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:03Z","_id":"556","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"},{"file":[{"file_id":"5600","checksum":"53c17082848e12f3c2e1b4185b578208","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2018-12-12T13:02:34Z","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","creator":"system","date_updated":"2020-07-14T12:47:05Z","file_size":1737958}],"day":"04","has_accepted_license":"1","year":"2018","datarep_id":"82","doi":"10.15479/AT:ISTA:82","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-319-24947-6_23","relation":"research_paper"}]},"date_published":"2018-01-04T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","contributor":[{"last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"}],"date_created":"2018-12-12T12:31:36Z","oa_version":"Published Version","abstract":[{"text":"Graph matching problems for large displacement optical flow of RGB-D images.","lang":"eng"}],"month":"01","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["001"],"date_updated":"2024-02-21T13:41:17Z","citation":{"ista":"Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology Austria, 10.15479/AT:ISTA:82.","chicago":"Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother. “Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:82.","apa":"Alhaija, H., Sellent, A., Kondermann, D., & Rother, C. (2018). Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:82","ama":"Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. 2018. doi:10.15479/AT:ISTA:82","ieee":"H. Alhaija, A. Sellent, D. Kondermann, and C. Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018.","short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","mla":"Alhaija, Hassan, et al. Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:82."},"file_date_updated":"2020-07-14T12:47:05Z","title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","department":[{"_id":"VlKo"}],"author":[{"first_name":"Hassan","last_name":"Alhaija","full_name":"Alhaija, Hassan"},{"full_name":"Sellent, Anita","last_name":"Sellent","first_name":"Anita"},{"last_name":"Kondermann","full_name":"Kondermann, Daniel","first_name":"Daniel"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"article_processing_charge":"No","_id":"5573","status":"public","keyword":["graph matching","quadratic assignment problem<"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"}},{"oa_version":"Submitted Version","abstract":[{"text":"Data on Austrian open access publication output at Emerald from 2013-2017 including data analysis.","lang":"ger"}],"month":"01","publisher":"Institute of Science and Technology Austria","oa":1,"day":"16","file":[{"file_name":"IST-2018-89-v1+1_Emerald_Austrian_Publications_2013-2017.zip","date_created":"2018-12-12T13:02:39Z","file_size":222011,"date_updated":"2020-07-14T12:47:06Z","creator":"system","checksum":"786b599abfae6c355dee87835f414549","file_id":"5604","content_type":"application/zip","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","year":"2018","datarep_id":"89","related_material":{"record":[{"id":"278","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/AT:ISTA:89","date_published":"2018-01-16T00:00:00Z","date_created":"2018-12-12T12:31:37Z","_id":"5577","status":"public","keyword":["Publication analysis","Bibliography","Open Access"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"citation":{"ista":"Villányi M. 2018. Emerald Austrian Publications 2013-2017, Institute of Science and Technology Austria, 10.15479/AT:ISTA:89.","chicago":"Villányi, Márton. “Emerald Austrian Publications 2013-2017.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:89.","ama":"Villányi M. Emerald Austrian Publications 2013-2017. 2018. doi:10.15479/AT:ISTA:89","apa":"Villányi, M. (2018). Emerald Austrian Publications 2013-2017. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:89","ieee":"M. Villányi, “Emerald Austrian Publications 2013-2017.” Institute of Science and Technology Austria, 2018.","short":"M. Villányi, (2018).","mla":"Villányi, Márton. Emerald Austrian Publications 2013-2017. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:89."},"date_updated":"2024-02-21T13:41:32Z","title":"Emerald Austrian Publications 2013-2017","file_date_updated":"2020-07-14T12:47:06Z","department":[{"_id":"E-Lib"}],"author":[{"first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","last_name":"Villányi"}],"article_processing_charge":"No"},{"file_date_updated":"2020-07-14T12:47:06Z","department":[{"_id":"E-Lib"}],"title":"IOP Austrian Publications 2012-2015","article_processing_charge":"No","author":[{"last_name":"Villányi","orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","first_name":"Márton"}],"ddc":["020"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Villányi, Márton. “IOP Austrian Publications 2012-2015.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:90.","ista":"Villányi M. 2018. 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However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? 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Data Check RSC Scopus vs. FWF, Institute of Science and Technology Austria, 10.15479/AT:ISTA:87.","chicago":"Villányi, Márton. “Data Check RSC Scopus vs. FWF.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:87."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"article_processing_charge":"No","author":[{"id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","first_name":"Márton","last_name":"Villányi","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426"}],"file_date_updated":"2020-07-14T12:47:05Z","title":"Data Check RSC Scopus vs. FWF","department":[{"_id":"E-Lib"}]},{"external_id":{"isi":["000434012100002"]},"article_processing_charge":"Yes","author":[{"orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicent","last_name":"Botella Soler","id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicent"},{"first_name":"Stephane","last_name":"Deny","full_name":"Deny, Stephane"},{"first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"title":"Nonlinear decoding of a complex movie from the mammalian retina","citation":{"ista":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057.","chicago":"Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.","ama":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057","apa":"Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1006057","ieee":"V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.","short":"V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).","mla":"Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425"},{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes"}],"article_number":"e1006057","date_created":"2018-12-11T11:45:39Z","doi":"10.1371/journal.pcbi.1006057","date_published":"2018-05-10T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"PLoS Computational Biology","day":"10","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:53Z","department":[{"_id":"GaTk"}],"date_updated":"2024-02-21T13:45:25Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"292","ec_funded":1,"issue":"5","volume":14,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","id":"5584","relation":"research_data"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5974","checksum":"3026f94d235219e15514505fdbadf34e","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-13T11:07:15Z","file_name":"2018_Plos_Botella_Soler.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:53Z","file_size":3460786}],"scopus_import":"1","intvolume":" 14","month":"05","abstract":[{"lang":"eng","text":"Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains."}],"oa_version":"Published Version"},{"ddc":["576"],"date_updated":"2024-02-21T13:44:45Z","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:27Z","_id":"438","status":"public","pubrep_id":"971","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2018-12-12T10:15:30Z","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","creator":"system","date_updated":"2020-07-14T12:46:27Z","file_size":5027978,"checksum":"3ff4f545c27e11a4cd20ccb30778793e","file_id":"5151","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5569"}]},"issue":"6","volume":46,"oa_version":"Published Version","abstract":[{"text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.","lang":"eng"}],"month":"04","intvolume":" 46","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.","ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931.","mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., & Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gky079","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018.","short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931."},"title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","author":[{"full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"full_name":"Vandervelde, Alexandra","last_name":"Vandervelde","first_name":"Alexandra"},{"first_name":"Tanino","last_name":"Albanese","full_name":"Albanese, Tanino"},{"first_name":"Lendert","last_name":"Gelens","full_name":"Gelens, Lendert"},{"full_name":"Moll, Isabella","last_name":"Moll","first_name":"Isabella"}],"external_id":{"isi":["000429009500021"]},"article_processing_charge":"Yes (in subscription journal)","project":[{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"day":"06","publication":"Nucleic Acids Research","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1093/nar/gky079","date_published":"2018-04-06T00:00:00Z","date_created":"2018-12-11T11:46:29Z","page":"2918-2931","quality_controlled":"1","publisher":"Oxford University Press","oa":1},{"date_created":"2018-12-11T11:44:47Z","doi":"10.7554/eLife.35684","date_published":"2018-08-13T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"eLife","day":"13","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","article_processing_charge":"No","external_id":{"isi":["000441388200001"]},"author":[{"last_name":"Picard","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cosseau","full_name":"Cosseau, Celine","first_name":"Celine"},{"full_name":"Ferré, Sabrina","last_name":"Ferré","first_name":"Sabrina"},{"last_name":"Quack","full_name":"Quack, Thomas","first_name":"Thomas"},{"last_name":"Grevelding","full_name":"Grevelding, Christoph","first_name":"Christoph"},{"last_name":"Couté","full_name":"Couté, Yohann","first_name":"Yohann"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"publist_id":"7792","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","citation":{"mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684","ieee":"M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684.","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e35684","volume":7,"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5586"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5695","checksum":"d6331d4385b1fffd6b47b45d5949d841","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_eLife_Picard.pdf","date_created":"2018-12-17T11:55:05Z","file_size":3158125,"date_updated":"2020-07-14T12:44:43Z","creator":"dernst"}],"scopus_import":"1","intvolume":" 7","month":"08","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"oa_version":"Published Version","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:44:43Z","date_updated":"2024-02-21T13:45:12Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"131"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. "}],"month":"03","publisher":"Institute of Science and Technology Austria","oa":1,"day":"29","file":[{"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","checksum":"6808748837b9afbbbabc2a356ca2b88a","file_id":"5590","date_updated":"2020-07-14T12:47:07Z","file_size":1142543971,"creator":"system","date_created":"2018-12-12T13:02:24Z","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d6d6cd07743038fe3a12352983fcf9dd","file_id":"5591","creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":702336,"date_created":"2018-12-12T13:02:25Z","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf"},{"checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","file_id":"5592","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","date_created":"2018-12-12T13:02:26Z","file_size":432,"date_updated":"2020-07-14T12:47:07Z","creator":"system"},{"file_size":986,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-98-v1+4_README.txt","date_created":"2018-12-12T13:02:26Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5593","checksum":"2a83b011012e21e934b4596285b1a183"}],"has_accepted_license":"1","datarep_id":"98","year":"2018","doi":"10.15479/AT:ISTA:98","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"292"}]},"date_published":"2018-03-29T00:00:00Z","date_created":"2018-12-12T12:31:39Z","_id":"5584","project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes"}],"status":"public","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98.","mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018."},"date_updated":"2024-02-21T13:45:26Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"title":"Nonlinear decoding of a complex movie from the mammalian retina","file_date_updated":"2020-07-14T12:47:07Z","author":[{"first_name":"Stephane","full_name":"Deny, Stephane","last_name":"Deny"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Botella-Soler, Vicente","last_name":"Botella-Soler","first_name":"Vicente"},{"last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"article_processing_charge":"No"},{"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"article_processing_charge":"No","external_id":{"isi":["000441753000007"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782."},"publisher":"Wiley","quality_controlled":"1","acknowledgement":"ERC, Grant/Award Number: 250152","doi":"10.1111/1755-0998.12782","date_published":"2018-09-01T00:00:00Z","date_created":"2018-12-11T11:45:37Z","page":"988 - 999","day":"01","publication":"Molecular Ecology Resources","isi":1,"year":"2018","status":"public","type":"journal_article","_id":"286","department":[{"_id":"NiBa"}],"date_updated":"2024-02-21T13:45:00Z","month":"09","intvolume":" 18","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. "}],"related_material":{"record":[{"status":"public","id":"5583","relation":"popular_science"}]},"issue":"5","volume":18,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"short":"B. Vicoso, (2018).","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109","mla":"Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109.","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109."},"date_updated":"2024-02-21T13:45:12Z","file_date_updated":"2020-07-14T12:47:08Z","department":[{"_id":"BeVi"}],"title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","article_processing_charge":"No","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"_id":"5586","keyword":["schistosoma","Z-chromosome","gene expression"],"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","file":[{"checksum":"e60b484bd6f55c08eb66a189cb72c923","file_id":"5601","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:02:35Z","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","date_updated":"2020-07-14T12:47:08Z","file_size":11918144,"creator":"system"}],"day":"24","datarep_id":"109","year":"2018","has_accepted_license":"1","date_created":"2018-12-12T12:31:40Z","contributor":[{"last_name":"Picard","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A"}],"doi":"10.15479/AT:ISTA:109","related_material":{"record":[{"id":"131","status":"public","relation":"research_paper"}]},"date_published":"2018-07-24T00:00:00Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)."}],"month":"07","oa":1,"publisher":"Institute of Science and Technology Austria"},{"department":[{"_id":"NiBa"}],"title":"Data and Python scripts supporting Python package FAPS","file_date_updated":"2020-07-14T12:47:07Z","article_processing_charge":"No","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:45:01Z","citation":{"ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","short":"T. Ellis, (2018).","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95."},"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5583","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_created":"2018-12-12T12:31:39Z","related_material":{"record":[{"relation":"research_paper","id":"286","status":"public"}]},"date_published":"2018-02-12T00:00:00Z","doi":"10.15479/AT:ISTA:95","file":[{"date_created":"2018-12-12T13:02:41Z","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":122048,"checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_id":"5606","access_level":"open_access","relation":"main_file","content_type":"text/csv"},{"creator":"system","file_size":235980,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","date_created":"2018-12-12T13:02:42Z","relation":"main_file","access_level":"open_access","content_type":"text/csv","checksum":"92347586ae4f8a6eb7c04354797bf314","file_id":"5607"},{"creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":311712,"date_created":"2018-12-12T13:02:43Z","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","access_level":"open_access","relation":"main_file","content_type":"text/csv","checksum":"3300813645a54e6c5c39f41917228354","file_id":"5608"},{"date_created":"2018-12-12T13:02:44Z","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_updated":"2020-07-14T12:47:07Z","file_size":342090,"creator":"system","checksum":"e739fc473567fd8f39438b445fc46147","file_id":"5609","content_type":"application/zip","access_level":"open_access","relation":"main_file"}],"day":"12","datarep_id":"95","year":"2018","has_accepted_license":"1","month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone."}]},{"title":"Time-lapse microscopy data","file_date_updated":"2020-07-14T12:47:04Z","department":[{"_id":"CaGu"}],"author":[{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7385","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["579"],"citation":{"chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","short":"T. Bergmiller, N. Nikolic, (2018)."},"date_updated":"2024-02-21T13:44:45Z","status":"public","keyword":["microscopy","microfluidics"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5569","doi":"10.15479/AT:ISTA:74","related_material":{"record":[{"status":"public","id":"438","relation":"research_paper"}]},"date_published":"2018-02-07T00:00:00Z","date_created":"2018-12-12T12:31:35Z","day":"07","file":[{"file_size":3558703796,"date_updated":"2020-07-14T12:47:04Z","creator":"system","file_name":"IST-2018-74-v1+2_15-11-05.zip","date_created":"2018-12-12T13:04:39Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637"},{"creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":1830422606,"date_created":"2018-12-12T13:04:55Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5638","checksum":"bf26649af310ef6892d68576515cde6d"},{"checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","file_id":"5639","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:05:11Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","date_updated":"2020-07-14T12:47:04Z","file_size":2140849248,"creator":"system"}],"has_accepted_license":"1","year":"2018","datarep_id":"74","month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}]},{"language":[{"iso":"eng"}],"file":[{"checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","file_id":"5728","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_NatureComm_DeMartino.pdf","date_created":"2018-12-17T16:44:28Z","file_size":1043205,"date_updated":"2020-07-14T12:45:06Z","creator":"dernst"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"status":"public","id":"5587","relation":"popular_science"}]},"volume":9,"issue":"1","oa_version":"Published Version","abstract":[{"text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells.","lang":"eng"}],"intvolume":" 9","month":"07","scopus_import":"1","ddc":["570"],"date_updated":"2024-02-21T13:45:39Z","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:06Z","_id":"161","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"Nature Communications","day":"30","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:57Z","date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41467-018-05417-9","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9"},"title":"Statistical mechanics for metabolic networks during steady state growth","external_id":{"isi":["000440149300021"]},"article_processing_charge":"No","publist_id":"7760","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino"},{"first_name":"Andersson Anna","last_name":"Mc","full_name":"Mc, Andersson Anna"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"article_number":"2988","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]},{"article_processing_charge":"No","author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:08Z","date_updated":"2024-02-21T13:45:39Z","citation":{"ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","apa":"De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","short":"D. De Martino, G. Tkačik, (2018).","mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62.","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"5587","ec_funded":1,"date_created":"2018-12-12T12:31:41Z","date_published":"2018-09-21T00:00:00Z","related_material":{"record":[{"status":"public","id":"161","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:62","datarep_id":"111","year":"2018","has_accepted_license":"1","file":[{"file_size":14376,"date_updated":"2020-07-14T12:47:08Z","creator":"system","file_name":"IST-2018-111-v1+1_CODES.zip","date_created":"2018-12-12T13:05:13Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_id":"5641","checksum":"97992e3e8cf8544ec985a48971708726"}],"day":"21","oa":1,"publisher":"Institute of Science and Technology Austria","month":"09","abstract":[{"text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).","lang":"eng"}],"oa_version":"Published Version"},{"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513","apa":"Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300513","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513."},"title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","author":[{"full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7274","external_id":{"isi":["000419356300024"]},"article_processing_charge":"No","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"day":"01","publication":"Genetics","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1534/genetics.117.300513","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:04Z","page":"365 - 375","_id":"542","status":"public","pubrep_id":"1058","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"date_updated":"2024-02-21T13:48:27Z","file_date_updated":"2020-07-14T12:46:50Z","department":[{"_id":"BeVi"}],"oa_version":"Published Version","abstract":[{"text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.","lang":"eng"}],"month":"01","intvolume":" 208","scopus_import":"1","file":[{"creator":"system","file_size":1311661,"date_updated":"2020-07-14T12:46:50Z","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","date_created":"2018-12-12T10:15:14Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5132","checksum":"2123845e7031a0cf043905be160f9e69"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":208,"related_material":{"record":[{"relation":"popular_science","id":"5571","status":"public"},{"id":"5572","status":"public","relation":"popular_science"}]},"ec_funded":1},{"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"7196","status":"public"},{"relation":"popular_science","id":"5559","status":"public"}]},"issue":"1","volume":1,"publication_status":"published","publication_identifier":{"issn":["2399-3642"]},"language":[{"iso":"eng"}],"file":[{"checksum":"a9db825fa3b64a51ff3de035ec973b3e","file_id":"5752","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_CommBiology_Pavlogiannis.pdf","date_created":"2018-12-18T13:37:04Z","creator":"dernst","file_size":1804194,"date_updated":"2020-07-14T12:47:10Z"}],"scopus_import":"1","intvolume":" 1","month":"06","abstract":[{"lang":"eng","text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"KrCh"}],"date_updated":"2024-02-21T13:48:42Z","ddc":["004","519","576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"1045","status":"public","_id":"5751","date_created":"2018-12-18T13:22:58Z","date_published":"2018-06-14T00:00:00Z","doi":"10.1038/s42003-018-0078-7","year":"2018","isi":1,"has_accepted_license":"1","publication":"Communications Biology","day":"14","oa":1,"publisher":"Springer Nature","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000461126500071"]},"author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","citation":{"mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"article_number":"71"},{"file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"citation":{"mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","short":"C. Fraisse, (2018).","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757."},"date_updated":"2024-02-21T13:59:18Z","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"type":"research_data","_id":"5757","related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]},"doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z","ec_funded":1,"contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"date_created":"2018-12-19T14:22:35Z","day":"19","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758","creator":"cfraisse","file_size":369837892,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS1.zip","date_created":"2018-12-19T14:19:52Z"},{"date_created":"2018-12-19T14:19:49Z","file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"creator":"cfraisse","file_id":"5759","checksum":"3592e467b4d8206650860b612d6e12f3","content_type":"application/zip","access_level":"open_access","relation":"main_file"},{"checksum":"c37ac5d5437c457338afc128c1240655","file_id":"5760","access_level":"open_access","relation":"main_file","content_type":"text/plain","date_created":"2018-12-19T14:19:49Z","file_name":"FileS3.txt","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":881133},{"access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"943dfd14da61817441e33e3e3cb8cdb9","file_id":"5761","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":883742,"date_created":"2018-12-19T14:19:49Z","file_name":"FileS4.txt"},{"relation":"main_file","access_level":"open_access","content_type":"text/plain","file_id":"5762","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","creator":"cfraisse","file_size":2495437,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS5.txt","date_created":"2018-12-19T14:19:49Z"},{"checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","content_type":"text/plain","access_level":"open_access","relation":"main_file","date_created":"2018-12-19T14:19:50Z","file_name":"FileS6.txt","date_updated":"2020-07-14T12:47:11Z","file_size":15913457,"creator":"cfraisse"},{"file_name":"FileS7.txt","date_created":"2018-12-19T14:19:50Z","file_size":2584120,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764","content_type":"text/plain","relation":"main_file","access_level":"open_access"},{"date_created":"2018-12-19T14:19:50Z","file_name":"FileS8.txt","date_updated":"2020-07-14T12:47:11Z","file_size":2446059,"creator":"cfraisse","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_id":"5765","content_type":"text/plain","access_level":"open_access","relation":"main_file"},{"content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5766","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_size":100737,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS9.txt","date_created":"2018-12-19T14:19:50Z"}],"has_accepted_license":"1","year":"2018","month":"12","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}]},{"publisher":"Institute of Science and Technology Austria","oa":1,"day":"12","has_accepted_license":"1","year":"2018","doi":"10.15479/AT:ISTA:TH_1040","date_published":"2018-07-12T00:00:00Z","date_created":"2018-12-11T11:44:53Z","page":"456","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040.","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","mla":"Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","apa":"Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040"},"title":"Dyson equation and eigenvalue statistics of random matrices","author":[{"first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes","last_name":"Alt"}],"publist_id":"7772","article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"month":"07","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2020-07-14T12:44:57Z","file_size":5801709,"creator":"dernst","date_created":"2019-04-08T13:55:20Z","file_name":"2018_thesis_Alt.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d4dad55a7513f345706aaaba90cb1bb8","file_id":"6241"},{"checksum":"d73fcf46300dce74c403f2b491148ab4","file_id":"6242","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"2018_thesis_Alt_source.zip","date_created":"2019-04-08T13:55:20Z","file_size":3802059,"date_updated":"2020-07-14T12:44:57Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"1677","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"550","status":"public"},{"relation":"part_of_dissertation","id":"6183","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"566"},{"relation":"part_of_dissertation","status":"public","id":"1010"},{"relation":"part_of_dissertation","id":"6240","status":"public"},{"id":"6184","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"_id":"149","status":"public","pubrep_id":"1040","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["515","519"],"supervisor":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-22T14:34:33Z","department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:44:57Z"},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":148,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]},"issue":"10","oa_version":"Preprint","abstract":[{"text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field.","lang":"eng"}],"intvolume":" 148","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09904"}],"scopus_import":"1","date_updated":"2024-02-28T13:01:59Z","department":[{"_id":"MiLe"}],"_id":"415","status":"public","type":"journal_article","article_type":"original","publication":"The Journal of Chemical Physics","day":"14","year":"2018","isi":1,"date_created":"2018-12-11T11:46:21Z","doi":"10.1063/1.5017591","date_published":"2018-03-14T00:00:00Z","acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.","short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018.","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591","apa":"Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591.","ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307."},"title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","article_processing_charge":"No","external_id":{"isi":["000427517200065"],"arxiv":["1711.09904"]},"author":[{"full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"publist_id":"7408","article_number":"104307","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","issue":"4","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","description":"News on IST Homepage"}]},"volume":37,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5744","checksum":"db75ebabe2ec432bf41389e614d6ef62","creator":"dernst","date_updated":"2020-07-14T12:44:45Z","file_size":22185016,"date_created":"2018-12-18T09:59:23Z","file_name":"2018_ACM_Jeschke.pdf"}],"publication_status":"published","intvolume":" 37","month":"07","alternative_title":["SIGGRAPH"],"scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2024-02-28T13:58:51Z","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","_id":"134","date_created":"2018-12-11T11:44:48Z","doi":"10.1145/3197517.3201336","date_published":"2018-07-30T00:00:00Z","publication":"ACM Transactions on Graphics","day":"30","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"ACM","title":"Water surface wavelets","external_id":{"isi":["000448185000055"]},"article_processing_charge":"No","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"first_name":"Matthias","full_name":"Mueller Fischer, Matthias","last_name":"Mueller Fischer"},{"first_name":"Nuttapong","last_name":"Chentanez","full_name":"Chentanez, Nuttapong"},{"last_name":"Macklin","full_name":"Macklin, Miles","first_name":"Miles"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publist_id":"7789","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336"},"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"94"},{"citation":{"chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"author":[{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin"},{"first_name":"Timur","full_name":"Tscherbul, Timur","last_name":"Tscherbul"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","article_number":"165301","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"year":"2018","isi":1,"publication":"Physical Review Letters","day":"16","date_created":"2019-04-17T10:53:38Z","doi":"10.1103/physrevlett.121.165301","date_published":"2018-10-16T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_updated":"2024-02-28T13:15:09Z","department":[{"_id":"MiLe"}],"_id":"6339","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","relation":"press_release","description":"News on IST Homepage"}]},"volume":121,"issue":"16","abstract":[{"text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"scopus_import":"1","intvolume":" 121","month":"10"},{"department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:14:53Z","status":"public","type":"journal_article","_id":"417","issue":"16","volume":121,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 121","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. "}],"title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","publist_id":"8025","author":[{"last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"last_name":"Tscherbul","full_name":"Tscherbul, Timur","first_name":"Timur"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"external_id":{"arxiv":["1803.07990"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301"},"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"article_number":"165301","date_published":"2018-10-16T00:00:00Z","doi":"10.1103/PhysRevLett.121.165301","date_created":"2018-12-11T11:46:22Z","day":"16","publication":"Physical Review Letters","year":"2018","quality_controlled":"1","publisher":"American Physical Society","oa":1},{"_id":"412","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-27T23:30:06Z","ddc":["580"],"file_date_updated":"2022-05-23T09:12:38Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 30","month":"04","publication_status":"published","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"language":[{"iso":"eng"}],"file":[{"checksum":"4e165e653b67d3f0684697f21aace5a1","file_id":"11406","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-05-23T09:12:38Z","file_name":"2018_PlantCell_Adamowski.pdf","creator":"dernst","date_updated":"2022-05-23T09:12:38Z","file_size":4407538}],"ec_funded":1,"issue":"3","volume":30,"related_material":{"record":[{"status":"public","id":"6269","relation":"dissertation_contains"}]},"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000429441400018"],"pmid":["29511054"]},"article_processing_charge":"No","publist_id":"7417","author":[{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"last_name":"De Jaeger","full_name":"De Jaeger, Geert","first_name":"Geert"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","year":"2018","isi":1,"has_accepted_license":"1","publication":"The Plant Cell","day":"09","page":"700 - 716","date_created":"2018-12-11T11:46:20Z","doi":"10.1105/tpc.17.00785","date_published":"2018-04-09T00:00:00Z"},{"oa":1,"publisher":"Society of Neuroscience","quality_controlled":"1","publication":"eNeuro","day":"27","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2019-02-03T22:59:16Z","doi":"10.1523/ENEURO.0087-18.2018","date_published":"2018-07-27T00:00:00Z","article_number":"e0087","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"I2072-B27","name":"Interneuron plasticity during spatial learning","_id":"257D4372-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.","ista":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087.","mla":"Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.","short":"D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).","ieee":"D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.","ama":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018","apa":"Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018"},"title":"Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning","article_processing_charge":"No","external_id":{"isi":["000443994700007"]},"author":[{"orcid":"0000-0002-8602-4374","full_name":"Rangel Guerrero, Dámaris K","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","first_name":"Dámaris K"},{"last_name":"Donnett","full_name":"Donnett, James G.","first_name":"James G."},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6251-1007","full_name":"Kovács, Krisztián","last_name":"Kovács","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task."}],"intvolume":" 5","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-05T12:48:36Z","file_name":"2018_ENeuro_Guerrero.pdf","date_updated":"2020-07-14T12:47:13Z","file_size":3746884,"creator":"dernst","file_id":"5921","checksum":"f4915d45fc7ad4648b7b7a13fdecca01","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6849"}]},"issue":"4","volume":5,"_id":"5914","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2024-03-27T23:30:10Z","department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:47:13Z"},{"project":[{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"}],"article_processing_charge":"No","external_id":{"pmid":["29567714"],"isi":["000428043600047"]},"author":[{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus"},{"last_name":"Assen","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"first_name":"Helga","last_name":"Schachner","full_name":"Schachner, Helga"},{"first_name":"Gabriele","full_name":"Asfour, Gabriele","last_name":"Asfour"},{"first_name":"Zsuzsanna","last_name":"Bagó Horváth","full_name":"Bagó Horváth, Zsuzsanna"},{"first_name":"Jens","last_name":"Stein","full_name":"Stein, Jens"},{"first_name":"Pavel","full_name":"Uhrin, Pavel","last_name":"Uhrin"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"}],"publist_id":"7428","title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","citation":{"chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.","ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662.","ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662","apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662","ieee":"M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018.","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","page":"1408 - 1411","date_created":"2018-12-11T11:46:16Z","doi":"10.1126/science.aal3662","date_published":"2018-03-23T00:00:00Z","year":"2018","isi":1,"publication":"Science","day":"23","article_type":"original","type":"journal_article","status":"public","_id":"402","department":[{"_id":"MiSi"}],"date_updated":"2024-03-27T23:30:09Z","main_file_link":[{"url":"https://doi.org/10.1126/science.aal3662","open_access":"1"}],"scopus_import":"1","intvolume":" 359","month":"03","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined."}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"6947","status":"public"}]},"volume":359,"issue":"6382","publication_status":"published","language":[{"iso":"eng"}]},{"publist_id":"7434","author":[{"last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara"}],"article_processing_charge":"No","title":"The branched chain amino acids in autism spectrum disorders ","citation":{"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.","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","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi: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.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","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.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25473368-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523"}],"page":"88","doi":"10.15479/AT:ISTA:th_992","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:14Z","has_accepted_license":"1","year":"2018","day":"01","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2021-02-11T23:30:15Z","department":[{"_id":"GaNo"}],"supervisor":[{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"date_updated":"2023-09-07T12:38:59Z","ddc":["570","616"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"992","_id":"395","related_material":{"record":[{"id":"1183","status":"public","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"checksum":"9f5231c96e0ad945040841a8630232da","file_id":"6217","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2018_Thesis_Tarlungeanu_source.docx","date_created":"2019-04-05T09:19:17Z","creator":"dernst","file_size":43684035,"date_updated":"2021-02-11T23:30:15Z"},{"creator":"dernst","date_updated":"2021-02-11T11:17:16Z","file_size":30511532,"date_created":"2019-04-05T09:19:17Z","file_name":"2018_Thesis_Tarlungeanu.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"0c33c370aa2010df5c552db57a6d01e9","file_id":"6218","embargo":"2018-03-15"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"03","abstract":[{"lang":"eng","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. "}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"oa_version":"Published Version"},{"title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","author":[{"id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","full_name":"Case, Matthew J","last_name":"Case"}],"publist_id":"8003","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Case, M. J. (2018). From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1032","ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032","short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018.","ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.","mla":"Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1032.","ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria.","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1032."},"date_published":"2018-06-27T00:00:00Z","doi":"10.15479/AT:ISTA:th_1032","date_created":"2018-12-11T11:44:22Z","page":"186","day":"27","has_accepted_license":"1","year":"2018","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2021-02-11T23:30:13Z","department":[{"_id":"RySh"}],"ddc":["571","576"],"supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:39:22Z","status":"public","pubrep_id":"1032","type":"dissertation","_id":"51","related_material":{"record":[{"relation":"part_of_dissertation","id":"682","status":"public"}]},"file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/msword","checksum":"dcc7b55619d8509dd62b8e99d6cdee44","file_id":"6251","creator":"dernst","file_size":141270528,"date_updated":"2021-02-11T23:30:13Z","file_name":"2018_Thesis_Case_Source.doc","date_created":"2019-04-09T07:16:26Z"},{"embargo":"2019-07-05","checksum":"f69fdd5c8709c4e618aa8c1a1221153d","file_id":"6252","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_Thesis_Case.pdf","date_created":"2019-04-09T07:16:23Z","file_size":15193621,"date_updated":"2021-02-11T11:17:14Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism.","lang":"eng"}]},{"day":"21","has_accepted_license":"1","year":"2018","doi":"10.15479/AT:ISTA:th1057","date_published":"2018-11-21T00:00:00Z","date_created":"2018-12-11T11:44:08Z","page":"1 - 139","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.","ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","mla":"Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057.","apa":"Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:10.15479/AT:ISTA:th1057","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018."},"title":"Role of genomic imprinting in cerebral cortex development","publist_id":"8046","author":[{"orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne"}],"article_processing_charge":"No","file":[{"checksum":"41fdbf5fdce312802935d88a8ad9932c","file_id":"6396","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Thesis_LaukoterSusanne_FINAL.docx","date_created":"2019-05-10T07:47:04Z","file_size":17949175,"date_updated":"2019-11-23T23:30:03Z","creator":"dernst"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"53001a9a0c9e570e598d861bb0af28aa","file_id":"6397","embargo":"2019-11-21","date_updated":"2021-02-11T11:17:16Z","file_size":21187245,"creator":"dernst","date_created":"2019-05-10T07:47:04Z","file_name":"Thesis_LaukoterSusanne_FINAL.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","oa_version":"Published Version","abstract":[{"text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.","lang":"eng"}],"month":"11","alternative_title":["ISTA Thesis"],"ddc":["570"],"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"date_updated":"2023-09-07T12:40:44Z","department":[{"_id":"SiHi"}],"file_date_updated":"2021-02-11T11:17:16Z","_id":"10","status":"public","pubrep_id":"1057","type":"dissertation"},{"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_created":"2019-04-05T09:23:11Z","file_name":"PhD_thesis_AlexLeithner_final_version.docx","creator":"dernst","date_updated":"2021-02-11T23:30:17Z","file_size":29027671,"checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","file_id":"6219","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"file_size":66045341,"date_updated":"2021-02-11T11:17:16Z","creator":"dernst","file_name":"PhD_thesis_AlexLeithner.pdf","date_created":"2019-04-05T09:23:11Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2019-04-15","file_id":"6220","checksum":"071f7476db29e41146824ebd0697cb10"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1321","status":"public"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"04","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"date_updated":"2023-09-07T12:39:44Z","ddc":["571","599","610"],"department":[{"_id":"MiSi"}],"file_date_updated":"2021-02-11T23:30:17Z","_id":"323","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"998","has_accepted_license":"1","year":"2018","day":"12","page":"99","date_published":"2018-04-12T00:00:00Z","doi":"10.15479/AT:ISTA:th_998","date_created":"2018-12-11T11:45:49Z","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe best boss one can imagine. I would also like to thank all current and past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m proud that I could be part of it. Furthermore, I would like to say ‘thank you’ to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to Federica Benvenuti for being part of my committee. I am also grateful to Jack \r\nMerrin in the nanofabrication facility and all the people working in the bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"mla":"Leithner, Alexander F. Branched Actin Networks in Dendritic Cell Biology. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_998.","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018.","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","apa":"Leithner, A. F. (2018). Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_998","ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:10.15479/AT:ISTA:th_998","chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_998.","ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F"}],"publist_id":"7542","article_processing_charge":"No","title":"Branched actin networks in dendritic cell biology"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:10.15479/AT:ISTA:th_930","ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","mla":"Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_930.","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930."},"title":"Identification and characterization of novel auxin-cytokinin cross-talk components","publist_id":"7277","author":[{"first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Hurny","orcid":"0000-0003-3638-1426","full_name":"Hurny, Andrej"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"01","has_accepted_license":"1","year":"2018","doi":"10.15479/AT:ISTA:th_930","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:03Z","page":"147","_id":"539","status":"public","pubrep_id":"930","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"supervisor":[{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:41:06Z","file_date_updated":"2020-12-02T23:30:08Z","department":[{"_id":"EvBe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"month":"01","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"0c9d6d1c80d9857e6e545213467bbcb2","file_id":"6226","creator":"dernst","file_size":28112114,"date_updated":"2020-12-02T23:30:08Z","file_name":"2018_Hurny_thesis_source.docx","date_created":"2019-04-05T09:37:56Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-07-10","file_id":"6227","checksum":"ecbe481a1413d270bd501b872c7ed54f","creator":"dernst","file_size":12524427,"date_updated":"2020-12-02T09:52:16Z","file_name":"2018_Hurny_thesis.pdf","date_created":"2019-04-05T09:37:55Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"1024","relation":"part_of_dissertation"}]}},{"_id":"48","pubrep_id":"1042","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["573"],"date_updated":"2023-09-07T12:42:44Z","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"}],"file_date_updated":"2021-02-11T23:30:22Z","department":[{"_id":"JoCs"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. "}],"month":"08","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"7db4415e435590fa33542c7b0a0321d7","file_id":"6236","creator":"dernst","date_updated":"2021-02-11T23:30:22Z","file_size":7666687,"date_created":"2019-04-08T13:36:01Z","file_name":"2018_Thesis_Gridchyn_source.docx"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-08-29","checksum":"f96f3fe8979f7b1e6db6acaca962b10c","file_id":"6237","creator":"dernst","file_size":6034153,"date_updated":"2021-02-11T11:17:18Z","file_name":"2018_Thesis_Gridchyn.pdf","date_created":"2019-04-08T13:36:01Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042.","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria.","mla":"Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042.","ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:10.15479/AT:ISTA:th_1042","apa":"Gridchyn, I. (2018). Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018."},"title":"Reactivation content is important for consolidation of spatial memory","article_processing_charge":"No","author":[{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","last_name":"Gridchyn","full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929"}],"publist_id":"8006","oa":1,"publisher":"Institute of Science and Technology Austria","day":"27","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:21Z","date_published":"2018-08-27T00:00:00Z","doi":"10.15479/AT:ISTA:th_1042","page":"104"},{"_id":"9","status":"public","pubrep_id":"1064","type":"dissertation","ddc":["570"],"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"}],"date_updated":"2023-09-07T12:43:10Z","file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"DaSi"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it."}],"month":"07","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","file_id":"6243","creator":"dernst","file_size":102737483,"date_updated":"2020-07-14T12:48:14Z","file_name":"2018_Thesis_Belyaeva_source.docx","date_created":"2019-04-08T14:13:12Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-11-19","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","file_id":"6244","creator":"dernst","file_size":88077843,"date_updated":"2021-02-11T11:17:16Z","file_name":"2018_Thesis_Belyaeva.pdf","date_created":"2019-04-08T14:14:08Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064.","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","mla":"Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064.","apa":"Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018."},"title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","author":[{"first_name":"Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","full_name":"Belyaeva, Vera","last_name":"Belyaeva"}],"publist_id":"8047","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"01","has_accepted_license":"1","year":"2018","doi":"10.15479/AT:ISTA:th1064","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:44:08Z","page":"96"},{"language":[{"iso":"eng"}],"file":[{"file_name":"2018_Thesis_McKenzie.pdf","date_created":"2019-04-09T14:12:40Z","creator":"dernst","file_size":4906420,"date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-24","checksum":"9d2c2dca04b00e485470c28b262af59a","file_id":"6267","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"checksum":"50b58c272899601bc6fd9642c4dc97f1","file_id":"6268","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2019-04-09T14:12:40Z","file_name":"2018_Thesis_McKenzie_source.docx","creator":"dernst","date_updated":"2020-07-14T12:47:25Z","file_size":5053545}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"new_edition","id":"7132","status":"public"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. "}],"month":"10","alternative_title":["ISTA Thesis"],"ddc":["571","573"],"date_updated":"2023-09-07T13:02:37Z","supervisor":[{"last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"HaJa"}],"_id":"6266","pubrep_id":"1055","status":"public","type":"dissertation","day":"31","year":"2018","has_accepted_license":"1","date_created":"2019-04-09T14:13:39Z","doi":"10.15479/at:ista:th_1055","date_published":"2018-10-31T00:00:00Z","page":"95","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","apa":"Mckenzie, C. (2018). Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th_1055","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055.","ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055."},"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","article_processing_charge":"No","author":[{"first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine","last_name":"Mckenzie"}]},{"oa_version":"Published Version","abstract":[{"text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation.","lang":"eng"}],"month":"06","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_id":"6238","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","embargo":"2019-06-25","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-04-08T13:42:26Z","file_name":"2018_Thesis_Capek.pdf","creator":"dernst","date_updated":"2021-02-11T11:17:17Z","file_size":31576521},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"6239","checksum":"876deb14067e638aba65d209668bd821","date_updated":"2021-02-11T23:30:21Z","file_size":38992956,"creator":"dernst","date_created":"2019-04-08T13:42:27Z","file_name":"2018_Thesis_Capek_source.docx"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"1100","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"661","status":"public"},{"id":"676","status":"public","relation":"part_of_dissertation"}]},"_id":"50","pubrep_id":"1031","status":"public","type":"dissertation","ddc":["570","591","596"],"date_updated":"2023-09-07T12:48:16Z","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-02-11T23:30:21Z","department":[{"_id":"CaHe"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"22","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:21Z","date_published":"2018-06-22T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1031","page":"95","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","apa":"Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031","ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031","mla":"Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031.","ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031."},"title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","article_processing_charge":"No","publist_id":"8004","author":[{"orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1059","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059."},"title":"The influence of sequence context on the evolution of bacterial gene expression","author":[{"last_name":"Steinrück","full_name":"Steinrück, Magdalena","orcid":"0000-0003-1229-9719","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8029","article_processing_charge":"No","day":"30","has_accepted_license":"1","year":"2018","date_published":"2018-10-30T00:00:00Z","doi":"10.15479/AT:ISTA:th1059","date_created":"2018-12-11T11:44:14Z","page":"109","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["576","579"],"supervisor":[{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:48:43Z","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:14Z","_id":"26","status":"public","pubrep_id":"1059","type":"dissertation","file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"5941","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","creator":"dernst","file_size":9190845,"date_updated":"2020-07-14T12:45:43Z","file_name":"Thesis_Steinrueck_final.docx","date_created":"2019-02-08T10:51:22Z"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2019-11-02","file_id":"5942","checksum":"3def8b7854c8b42d643597ce0215efac","file_size":7521973,"date_updated":"2021-02-11T11:17:14Z","creator":"dernst","file_name":"Thesis_Steinrueck_final.pdf","date_created":"2019-02-08T10:51:22Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"704","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"month":"10","alternative_title":["ISTA Thesis"]},{"status":"public","type":"journal_article","_id":"5816","department":[{"_id":"GeKa"}],"date_updated":"2024-03-27T23:30:26Z","month":"11","intvolume":" 89","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"oa_version":"Preprint","abstract":[{"text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field.","lang":"eng"}],"volume":89,"issue":"11","related_material":{"record":[{"status":"public","id":"10058","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00346748"]},"publication_status":"published","article_number":"114701","title":"30 GHz-voltage controlled oscillator operating at 4 K","author":[{"first_name":"Arne","last_name":"Hollmann","full_name":"Hollmann, Arne"},{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"Maciej","last_name":"Kucharski","full_name":"Kucharski, Maciej"},{"first_name":"Dietmar","last_name":"Kissinger","full_name":"Kissinger, Dietmar"},{"full_name":"Fischer, Gunter","last_name":"Fischer","first_name":"Gunter"},{"first_name":"Lars R.","last_name":"Schreiber","full_name":"Schreiber, Lars R."}],"article_processing_charge":"No","external_id":{"isi":["000451735700054"],"arxiv":["1804.09522"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:10.1063/1.5038258.","short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.","ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258.","ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701."},"publisher":"AIP Publishing","quality_controlled":"1","oa":1,"doi":"10.1063/1.5038258","date_published":"2018-11-01T00:00:00Z","date_created":"2019-01-10T14:22:23Z","day":"01","publication":"Review of Scientific Instruments","isi":1,"year":"2018"},{"title":"Genetic determinants of antibiotic resistance evolution","article_processing_charge":"No","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072","ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072","short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","mla":"Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072."},"date_created":"2019-04-09T13:57:15Z","doi":"10.15479/AT:ISTA:th1072","date_published":"2018-12-28T00:00:00Z","page":"91","day":"28","year":"2018","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T11:17:17Z","department":[{"_id":"ToBo"}],"ddc":["570","576","579"],"date_updated":"2023-09-22T09:20:37Z","supervisor":[{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"}],"status":"public","type":"dissertation","_id":"6263","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1619"},{"status":"public","id":"696","relation":"part_of_dissertation"},{"status":"public","id":"1027","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fc60585c9eaad868ac007004ef130908","file_id":"6264","embargo":"2020-01-25","date_updated":"2021-02-11T11:17:17Z","file_size":5656866,"creator":"dernst","date_created":"2019-04-09T13:49:24Z","file_name":"2018_Thesis_Lukacisinova.pdf"},{"date_created":"2019-04-09T13:49:23Z","file_name":"2018_Thesis_Lukacisinova_source.docx","date_updated":"2020-07-14T12:47:25Z","file_size":5168054,"creator":"dernst","checksum":"264057ec0a92ab348cc83b41f021ba92","file_id":"6265","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Antibiotic resistance can emerge spontaneously through genomic mutation and render treatment ineffective. To counteract this process, in addition to the discovery and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its determinantsis needed. To address this challenge, this thesisuncoversnew genetic determinants of resistance evolvability using a customized robotic setup, exploressystematic ways in which resistance evolution is perturbed due to dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order to identify them, we first developedan automated high-throughput feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic concentration. We implementedthis protocol on a customized liquid handling robot and propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100 generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more compared to less sensitive ones. Our data uncover that deletions of certain genes which do not affect mutation rate,including efflux pump components, a chaperone and severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution. Sequencing analysis of evolved populations indicates that epistasis with resistance mutations is the most likelyexplanation. This work could inspire treatment strategies in which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model, toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations. We show that in silicothis also leads to slower resistance evolution. We see and confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier –a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under periodic selectionakin to clinical treatment. We set up a deterministic infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and evaluate various treatment schemes in how well they maintain a stress-induced mutator allele. In particular,a high diversity of stresses is crucial for the persistence of the mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. "}]},{"acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"03","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:56Z","file_size":2251222,"creator":"system","date_created":"2018-12-12T10:11:48Z","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4905","checksum":"7d9d28b915159078a4ca7add568010e8"}],"ec_funded":1,"related_material":{"record":[{"id":"6530","relation":"research_paper"},{"relation":"research_paper","id":"6543"},{"status":"public","id":"11193","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"6546","status":"public"}]},"volume":8,"issue":"3","_id":"544","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"990","status":"public","date_updated":"2024-03-27T23:30:29Z","ddc":["570"],"department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:46:56Z","acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","year":"2018","has_accepted_license":"1","isi":1,"publication":"G3: Genes, Genomes, Genetics","day":"01","page":"845 - 857","date_created":"2018-12-11T11:47:05Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1534/g3.117.300452","project":[{"grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion"},{"_id":"2637E9C0-B435-11E9-9278-68D0E5697425","name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","grant_number":"LSC16-021 "},{"name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:10.1534/g3.117.300452.","short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","ieee":"A. György et al., “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 2018;8(3):845-857. doi:10.1534/g3.117.300452","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452","chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/g3.117.300452.","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000426693300011"]},"author":[{"last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","full_name":"Ratheesh, Aparna","orcid":"0000-0001-7190-0776","last_name":"Ratheesh"},{"last_name":"Valosková","full_name":"Valosková, Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"full_name":"Belyaeva, Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera"},{"id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Wachner","full_name":"Wachner, Stephanie"},{"full_name":"Matsubayashi, Yutaka","last_name":"Matsubayashi","first_name":"Yutaka"},{"first_name":"Besaiz","full_name":"Sanchez Sanchez, Besaiz","last_name":"Sanchez Sanchez"},{"first_name":"Brian","last_name":"Stramer","full_name":"Stramer, Brian"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus"}],"publist_id":"7271","title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues"}]