[{"title":"Infinite-duration bidding games","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","last_name":"Avni","full_name":"Avni, Guy"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","last_name":"Chonev","full_name":"Chonev, Ventsislav K"}],"publisher":"ACM","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"article_processing_charge":"No","quality_controlled":"1","_id":"6752","type":"journal_article","arxiv":1,"scopus_import":"1","abstract":[{"text":"Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players.","lang":"eng"}],"publication_identifier":{"issn":["00045411"],"eissn":["1557735X"]},"citation":{"mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” <i>Journal of the ACM</i>, vol. 66, no. 4, 31, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3340295\">10.1145/3340295</a>.","apa":"Avni, G., Henzinger, T. A., &#38; Chonev, V. K. (2019). Infinite-duration bidding games. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3340295\">https://doi.org/10.1145/3340295</a>","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3340295\">https://doi.org/10.1145/3340295</a>.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. <i>Journal of the ACM</i>. 2019;66(4). doi:<a href=\"https://doi.org/10.1145/3340295\">10.1145/3340295</a>","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” <i>Journal of the ACM</i>, vol. 66, no. 4. ACM, 2019.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31."},"publication_status":"published","project":[{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","call_identifier":"FWF"}],"issue":"4","oa":1,"date_updated":"2023-08-29T07:02:13Z","article_number":"31","intvolume":"        66","month":"07","date_published":"2019-07-16T00:00:00Z","year":"2019","external_id":{"arxiv":["1705.01433"],"isi":["000487714900008"]},"day":"16","status":"public","date_created":"2019-08-04T21:59:16Z","volume":66,"isi":1,"oa_version":"Preprint","related_material":{"record":[{"id":"950","status":"public","relation":"earlier_version"}]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01433"}],"doi":"10.1145/3340295","publication":"Journal of the ACM"},{"status":"public","day":"01","date_created":"2019-08-04T21:59:18Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"pmid":1,"volume":11,"isi":1,"oa_version":"Published Version","doi":"10.1093/gbe/evz133","publication":"Genome biology and evolution","issue":"7","oa":1,"acknowledged_ssus":[{"_id":"CampIT"}],"date_updated":"2023-08-29T06:53:58Z","month":"07","intvolume":"        11","date_published":"2019-07-01T00:00:00Z","year":"2019","external_id":{"isi":["000484039500018"],"pmid":["31273378"]},"page":"1909-1922","quality_controlled":"1","_id":"6755","type":"journal_article","file_date_updated":"2020-07-14T12:47:39Z","abstract":[{"lang":"eng","text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region."}],"scopus_import":"1","publication_identifier":{"eissn":["1759-6653"]},"citation":{"short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","ieee":"M. A. L. Picard <i>et al.</i>, “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 7. Oxford Academic Press, pp. 1909–1922, 2019.","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome biology and evolution</i>. 2019;11(7):1909-1922. doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>","chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>. Oxford Academic Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome Biology and Evolution</i>. Oxford Academic Press. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 7, Oxford Academic Press, 2019, pp. 1909–22, doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>."},"publication_status":"published","file":[{"file_name":"2019_GenomeBiology_Picard.pdf","date_created":"2019-08-05T07:55:02Z","date_updated":"2020-07-14T12:47:39Z","file_id":"6765","content_type":"application/pdf","file_size":580205,"creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"f9e8f6863a406dcc5a36b2be001c138c"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Picard, Marion A L","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","orcid":"0000-0002-8101-2518"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roquis, David","last_name":"Roquis","first_name":"David"},{"full_name":"Bulla, Ingo","first_name":"Ingo","last_name":"Bulla"},{"full_name":"Augusto, Ronaldo C.","first_name":"Ronaldo C.","last_name":"Augusto"},{"first_name":"Nathalie","last_name":"Arancibia","full_name":"Arancibia, Nathalie"},{"full_name":"Grunau, Christoph","last_name":"Grunau","first_name":"Christoph"},{"full_name":"Boissier, Jérôme","last_name":"Boissier","first_name":"Jérôme"},{"first_name":"Céline","last_name":"Cosseau","full_name":"Cosseau, Céline"}],"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","publisher":"Oxford Academic Press","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"article_processing_charge":"No"},{"volume":627,"ddc":["520","530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-08-04T21:59:18Z","status":"public","day":"17","doi":"10.1051/0004-6361/201834916","publication":"Astronomy and Astrophysics","isi":1,"oa_version":"Published Version","month":"07","intvolume":"       627","date_published":"2019-07-17T00:00:00Z","article_number":"A163","date_updated":"2023-08-29T07:01:48Z","oa":1,"external_id":{"isi":["000475839300003"],"arxiv":["1812.07678"]},"year":"2019","publication_identifier":{"issn":["00046361"],"eissn":["14320746"]},"citation":{"mla":"Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” <i>Astronomy and Astrophysics</i>, vol. 627, A163, EDP Sciences, 2019, doi:<a href=\"https://doi.org/10.1051/0004-6361/201834916\">10.1051/0004-6361/201834916</a>.","apa":"Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman, A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations in the cosmic microwave background. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201834916\">https://doi.org/10.1051/0004-6361/201834916</a>","chicago":"Pranav, Pratyush, Robert J. Adler, Thomas Buchert, Herbert Edelsbrunner, Bernard J.T. Jones, Armin Schwartzman, Hubert Wagner, and Rien Van De Weygaert. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” <i>Astronomy and Astrophysics</i>. EDP Sciences, 2019. <a href=\"https://doi.org/10.1051/0004-6361/201834916\">https://doi.org/10.1051/0004-6361/201834916</a>.","ama":"Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature fluctuations in the cosmic microwave background. <i>Astronomy and Astrophysics</i>. 2019;627. doi:<a href=\"https://doi.org/10.1051/0004-6361/201834916\">10.1051/0004-6361/201834916</a>","short":"P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman, H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019).","ista":"Pranav P, Adler RJ, Buchert T, Edelsbrunner H, Jones BJT, Schwartzman A, Wagner H, Van De Weygaert R. 2019. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 627, A163.","ieee":"P. Pranav <i>et al.</i>, “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” <i>Astronomy and Astrophysics</i>, vol. 627. EDP Sciences, 2019."},"type":"journal_article","file_date_updated":"2020-07-14T12:47:39Z","arxiv":1,"abstract":[{"text":"We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.","lang":"eng"}],"scopus_import":"1","_id":"6756","quality_controlled":"1","project":[{"name":"Toward Computational Information Topology","_id":"265683E4-B435-11E9-9278-68D0E5697425","grant_number":"M62909-18-1-2038"},{"grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","has_accepted_license":"1","publisher":"EDP Sciences","file":[{"file_name":"2019_AstronomyAstrophysics_Pranav.pdf","date_created":"2019-08-05T08:08:59Z","date_updated":"2020-07-14T12:47:39Z","file_size":14420451,"creator":"dernst","content_type":"application/pdf","file_id":"6766","relation":"main_file","checksum":"83b9209ed9eefbdcefd89019c5a97805","access_level":"open_access"}],"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","author":[{"full_name":"Pranav, Pratyush","last_name":"Pranav","first_name":"Pratyush"},{"full_name":"Adler, Robert J.","first_name":"Robert J.","last_name":"Adler"},{"full_name":"Buchert, Thomas","first_name":"Thomas","last_name":"Buchert"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Jones, Bernard J.T.","last_name":"Jones","first_name":"Bernard J.T."},{"full_name":"Schwartzman, Armin","last_name":"Schwartzman","first_name":"Armin"},{"last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"},{"full_name":"Van De Weygaert, Rien","last_name":"Van De Weygaert","first_name":"Rien"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"article_type":"original"},{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"article_processing_charge":"No","author":[{"full_name":"Jelínek, Vít","last_name":"Jelínek","first_name":"Vít"},{"full_name":"Töpfer, Martin","last_name":"Töpfer","id":"4B865388-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"title":"On grounded L-graphs and their relatives","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2019_eJourCombinatorics_Jelinek.pdf","date_created":"2019-08-05T06:46:55Z","date_updated":"2020-07-14T12:47:39Z","file_id":"6764","content_type":"application/pdf","file_size":533697,"creator":"dernst","checksum":"20fc366fc6683ef0b074a019b73a663a","access_level":"open_access","relation":"main_file"}],"publisher":"Electronic Journal of Combinatorics","has_accepted_license":"1","publication_status":"published","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"quality_controlled":"1","_id":"6759","abstract":[{"text":"We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions.","lang":"eng"}],"scopus_import":"1","arxiv":1,"file_date_updated":"2020-07-14T12:47:39Z","type":"journal_article","publication_identifier":{"eissn":["10778926"]},"citation":{"apa":"Jelínek, V., &#38; Töpfer, M. (2019). On grounded L-graphs and their relatives. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/8096\">https://doi.org/10.37236/8096</a>","mla":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” <i>Electronic Journal of Combinatorics</i>, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:<a href=\"https://doi.org/10.37236/8096\">10.37236/8096</a>.","ama":"Jelínek V, Töpfer M. On grounded L-graphs and their relatives. <i>Electronic Journal of Combinatorics</i>. 2019;26(3). doi:<a href=\"https://doi.org/10.37236/8096\">10.37236/8096</a>","ieee":"V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” <i>Electronic Journal of Combinatorics</i>, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019.","ista":"Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17.","short":"V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).","chicago":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2019. <a href=\"https://doi.org/10.37236/8096\">https://doi.org/10.37236/8096</a>."},"year":"2019","external_id":{"arxiv":["1808.04148"]},"oa":1,"issue":"3","date_updated":"2022-03-18T12:32:02Z","article_number":"P3.17","date_published":"2019-07-19T00:00:00Z","intvolume":"        26","month":"07","oa_version":"Published Version","ec_funded":1,"publication":"Electronic Journal of Combinatorics","doi":"10.37236/8096","status":"public","day":"19","date_created":"2019-08-04T21:59:20Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"volume":26},{"doi":"10.1137/18M1207272","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"publication":"Multiscale Modeling and Simulation","isi":1,"oa_version":"Preprint","volume":17,"day":"16","status":"public","date_created":"2019-08-04T21:59:21Z","page":"926-947","external_id":{"arxiv":["1808.04200"],"isi":["000487931800002"]},"year":"2019","intvolume":"        17","month":"07","date_published":"2019-07-16T00:00:00Z","issue":"3","oa":1,"date_updated":"2023-09-05T15:05:45Z","publication_status":"published","type":"journal_article","abstract":[{"lang":"eng","text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size."}],"scopus_import":"1","arxiv":1,"citation":{"ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. <i>Multiscale Modeling and Simulation</i>. 2019;17(3):926-947. doi:<a href=\"https://doi.org/10.1137/18M1207272\">10.1137/18M1207272</a>","ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” <i>Multiscale Modeling and Simulation</i>, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” <i>Multiscale Modeling and Simulation</i>. SIAM, 2019. <a href=\"https://doi.org/10.1137/18M1207272\">https://doi.org/10.1137/18M1207272</a>.","apa":"Friesecke, G., &#38; Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. <i>Multiscale Modeling and Simulation</i>. SIAM. <a href=\"https://doi.org/10.1137/18M1207272\">https://doi.org/10.1137/18M1207272</a>","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” <i>Multiscale Modeling and Simulation</i>, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:<a href=\"https://doi.org/10.1137/18M1207272\">10.1137/18M1207272</a>."},"publication_identifier":{"issn":["15403459"],"eissn":["15403467"]},"quality_controlled":"1","_id":"6762","department":[{"_id":"JuFi"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"SIAM","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Friesecke","first_name":"Gero","full_name":"Friesecke, Gero"},{"full_name":"Kniely, Michael","first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","last_name":"Kniely"}],"title":"New optimal control problems in density functional theory motivated by photovoltaics"},{"pmid":1,"volume":15,"date_created":"2019-08-04T21:59:21Z","status":"public","day":"15","doi":"10.1039/c9sm00756c","publication":"Soft Matter","isi":1,"oa_version":"None","month":"07","intvolume":"        15","date_published":"2019-07-15T00:00:00Z","date_updated":"2023-08-29T06:53:34Z","issue":"29","external_id":{"pmid":["31305853"],"isi":["000476909200002"]},"page":"5804-5809","year":"2019","citation":{"apa":"Khattak, H. K., Waitukaitis, S. R., &#38; Slepkov, A. D. (2019). Microwave induced mechanical activation of hydrogel dimers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c9sm00756c\">https://doi.org/10.1039/c9sm00756c</a>","mla":"Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” <i>Soft Matter</i>, vol. 15, no. 29, Royal Society of Chemistry, 2019, pp. 5804–09, doi:<a href=\"https://doi.org/10.1039/c9sm00756c\">10.1039/c9sm00756c</a>.","ama":"Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation of hydrogel dimers. <i>Soft Matter</i>. 2019;15(29):5804-5809. doi:<a href=\"https://doi.org/10.1039/c9sm00756c\">10.1039/c9sm00756c</a>","short":"H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.","ieee":"H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical activation of hydrogel dimers,” <i>Soft Matter</i>, vol. 15, no. 29. Royal Society of Chemistry, pp. 5804–5809, 2019.","ista":"Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809.","chicago":"Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” <i>Soft Matter</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c9sm00756c\">https://doi.org/10.1039/c9sm00756c</a>."},"publication_identifier":{"eissn":["17446848"],"issn":["1744683X"]},"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.\r\nWe show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics."}],"_id":"6763","quality_controlled":"1","publication_status":"published","publisher":"Royal Society of Chemistry","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Hamza K.","last_name":"Khattak","full_name":"Khattak, Hamza K."},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"},{"full_name":"Slepkov, Aaron D.","first_name":"Aaron D.","last_name":"Slepkov"}],"title":"Microwave induced mechanical activation of hydrogel dimers","article_processing_charge":"No","department":[{"_id":"ScWa"}],"language":[{"iso":"eng"}],"article_type":"original"},{"department":[{"_id":"JiFr"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","title":"Evolution of fast root gravitropism in seed plants","author":[{"orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou"},{"first_name":"G","last_name":"Xiao","full_name":"Xiao, G"},{"last_name":"Wang","first_name":"X","full_name":"Wang, X"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","full_name":"Zhang, Xixi"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2019_NatureComm_Zhang.pdf","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:09:20Z","file_id":"6798","content_type":"application/pdf","file_size":6406141,"creator":"dernst","checksum":"d2c654fdb97f33078f606fe0c298bf6e","relation":"main_file","access_level":"open_access"}],"publication_status":"published","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"abstract":[{"text":"An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips\r\nalong with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:47:40Z","publication_identifier":{"issn":["2041-1723"]},"citation":{"chicago":"Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of Fast Root Gravitropism in Seed Plants.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-11471-8\">https://doi.org/10.1038/s41467-019-11471-8</a>.","short":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019).","ieee":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root gravitropism in seed plants,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","ista":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480.","ama":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-11471-8\">10.1038/s41467-019-11471-8</a>","mla":"Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.” <i>Nature Communications</i>, vol. 10, 3480, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-11471-8\">10.1038/s41467-019-11471-8</a>.","apa":"Zhang, Y., Xiao, G., Wang, X., Zhang, X., &#38; Friml, J. (2019). Evolution of fast root gravitropism in seed plants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-11471-8\">https://doi.org/10.1038/s41467-019-11471-8</a>"},"quality_controlled":"1","_id":"6778","external_id":{"pmid":["31375675"],"isi":["000478576500012"]},"year":"2019","article_number":"3480","date_published":"2019-08-02T00:00:00Z","month":"08","intvolume":"        10","oa":1,"date_updated":"2023-08-29T07:02:44Z","publication":"Nature Communications","doi":"10.1038/s41467-019-11471-8","oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/"}]},"volume":10,"pmid":1,"status":"public","day":"02","date_created":"2019-08-09T08:46:26Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"]},{"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"citation":{"apa":"Suri, B., Pallantla, R. K., Schatz, M. F., &#38; Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.100.013112\">https://doi.org/10.1103/physreve.100.013112</a>","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” <i>Physical Review E</i>, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physreve.100.013112\">10.1103/physreve.100.013112</a>.","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” <i>Physical Review E</i>, vol. 100, no. 1. American Physical Society, 2019.","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. <i>Physical Review E</i>. 2019;100(1). doi:<a href=\"https://doi.org/10.1103/physreve.100.013112\">10.1103/physreve.100.013112</a>","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” <i>Physical Review E</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physreve.100.013112\">https://doi.org/10.1103/physreve.100.013112</a>."},"arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace."}],"type":"journal_article","_id":"6779","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"publication_status":"published","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Suri","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","full_name":"Suri, Balachandra"},{"full_name":"Pallantla, Ravi Kumar","first_name":"Ravi Kumar","last_name":"Pallantla"},{"last_name":"Schatz","first_name":"Michael F.","full_name":"Schatz, Michael F."},{"full_name":"Grigoriev, Roman O.","last_name":"Grigoriev","first_name":"Roman O."}],"title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","article_processing_charge":"No","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"article_type":"original","volume":100,"date_created":"2019-08-09T09:40:41Z","ddc":["532"],"day":"25","status":"public","publication":"Physical Review E","doi":"10.1103/physreve.100.013112","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.05860"}],"oa_version":"Preprint","ec_funded":1,"isi":1,"date_published":"2019-07-25T00:00:00Z","month":"07","intvolume":"       100","article_number":"013112","date_updated":"2024-02-28T13:13:00Z","oa":1,"issue":"1","external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"year":"2019"},{"file":[{"file_name":"oopsla-2019.pdf","date_created":"2019-08-12T15:40:57Z","date_updated":"2020-07-14T12:47:40Z","file_id":"6807","content_type":"application/pdf","creator":"akafshda","file_size":1024643,"access_level":"open_access","relation":"main_file","checksum":"3482d8ace6fb4991eb7810e3b70f1b9f"},{"access_level":"open_access","checksum":"4e5a6fb2b59a75222a4e8335a5a60eac","relation":"main_file","file_id":"7821","content_type":"application/pdf","creator":"dernst","file_size":538579,"date_updated":"2020-07-14T12:47:40Z","date_created":"2020-05-12T15:15:14Z","file_name":"2019_ACM_Huang.pdf"}],"author":[{"full_name":"Huang, Mingzhang","first_name":"Mingzhang","last_name":"Huang"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"}],"title":"Modular verification for almost-sure termination of probabilistic programs","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"ACM","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"article_processing_charge":"No","quality_controlled":"1","_id":"6780","file_date_updated":"2020-07-14T12:47:40Z","type":"conference","arxiv":1,"abstract":[{"text":"In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a\r\ngiven probabilistic program terminates with probability 1. Scalable approaches for program analysis often\r\nrely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure\r\ntermination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic programs.\r\nBesides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a\r\nsound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel\r\nnotion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat are linear and show that they can be synthesized in polynomial time. Finally, we present experimental\r\nresults on a variety of benchmarks and several natural examples that model various types of nested while\r\nloops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination property","lang":"eng"}],"citation":{"chicago":"Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360555\">https://doi.org/10.1145/3360555</a>.","short":"M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , ACM, 2019.","ieee":"M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification for almost-sure termination of probabilistic programs,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, Athens, Greece, 2019, vol. 3.","ista":"Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for almost-sure termination of probabilistic programs. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 129.","ama":"Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure termination of probabilistic programs. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360555\">10.1145/3360555</a>","mla":"Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, vol. 3, 129, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360555\">10.1145/3360555</a>.","apa":"Huang, M., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2019). Modular verification for almost-sure termination of probabilistic programs. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360555\">https://doi.org/10.1145/3360555</a>"},"publication_status":"published","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"oa":1,"date_updated":"2025-06-02T08:53:47Z","article_number":"129","month":"10","intvolume":"         3","date_published":"2019-10-01T00:00:00Z","year":"2019","license":"https://creativecommons.org/licenses/by-nc/4.0/","conference":{"location":"Athens, Greece","end_date":"2019-10-25","start_date":"2019-10-23","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications"},"external_id":{"arxiv":["1901.06087"]},"day":"01","status":"public","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["000"],"date_created":"2019-08-09T09:54:20Z","volume":3,"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"doi":"10.1145/3360555","publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications "},{"publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1007168","related_material":{"record":[{"relation":"research_data","status":"public","id":"9786"}]},"oa_version":"Published Version","isi":1,"volume":15,"date_created":"2019-08-11T21:59:19Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"day":"02","status":"public","external_id":{"isi":["000481577700032"]},"year":"2019","date_published":"2019-07-02T00:00:00Z","intvolume":"        15","month":"07","article_number":"e1007168","date_updated":"2023-08-29T07:10:06Z","oa":1,"issue":"7","project":[{"grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","_id":"251D65D8-B435-11E9-9278-68D0E5697425"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011"}],"publication_status":"published","publication_identifier":{"eissn":["1553-7358"]},"citation":{"mla":"Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” <i>PLoS Computational Biology</i>, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">10.1371/journal.pcbi.1007168</a>.","apa":"Ruess, J., Pleska, M., Guet, C. C., &#38; Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">https://doi.org/10.1371/journal.pcbi.1007168</a>","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">https://doi.org/10.1371/journal.pcbi.1007168</a>.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” <i>PLoS Computational Biology</i>, vol. 15, no. 7. Public Library of Science, 2019.","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. <i>PLoS Computational Biology</i>. 2019;15(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">10.1371/journal.pcbi.1007168</a>"},"abstract":[{"lang":"eng","text":"Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems."}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:40Z","type":"journal_article","_id":"6784","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Public Library of Science","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","last_name":"Ruess","full_name":"Ruess, Jakob"},{"orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros"},{"full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","file":[{"file_size":2200003,"creator":"dernst","file_id":"6803","content_type":"application/pdf","access_level":"open_access","checksum":"7ded4721b41c2a0fc66a1c634540416a","relation":"main_file","file_name":"2019_PlosComputBiology_Ruess.pdf","date_created":"2019-08-12T12:27:26Z","date_updated":"2020-07-14T12:47:40Z"}]},{"oa_version":"Published Version","isi":1,"publication":"Physical Review X","doi":"10.1103/PhysRevX.9.021026","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-08-11T21:59:20Z","ddc":["530"],"status":"public","day":"08","volume":9,"year":"2019","external_id":{"arxiv":["1807.11238"],"isi":["000467402900001"]},"date_updated":"2024-02-28T13:12:48Z","oa":1,"issue":"2","date_published":"2019-05-08T00:00:00Z","month":"05","intvolume":"         9","article_number":"021026","project":[{"grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","_id":"6786","quality_controlled":"1","citation":{"ama":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. <i>Physical Review X</i>. 2019;9(2). doi:<a href=\"https://doi.org/10.1103/PhysRevX.9.021026\">10.1103/PhysRevX.9.021026</a>","short":"C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).","ieee":"C. Hubert <i>et al.</i>, “Attractive dipolar coupling between stacked exciton fluids,” <i>Physical Review X</i>, vol. 9, no. 2. American Physical Society, 2019.","ista":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026.","chicago":"Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” <i>Physical Review X</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevX.9.021026\">https://doi.org/10.1103/PhysRevX.9.021026</a>.","apa":"Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.9.021026\">https://doi.org/10.1103/PhysRevX.9.021026</a>","mla":"Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” <i>Physical Review X</i>, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevX.9.021026\">10.1103/PhysRevX.9.021026</a>."},"publication_identifier":{"eissn":["2160-3308"]},"arxiv":1,"abstract":[{"text":"Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations.","lang":"eng"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:40Z","type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MiLe"}],"title":"Attractive dipolar coupling between stacked exciton fluids","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hubert","first_name":"Colin","full_name":"Hubert, Colin"},{"first_name":"Yifat","last_name":"Baruchi","full_name":"Baruchi, Yifat"},{"full_name":"Mazuz-Harpaz, Yotam","first_name":"Yotam","last_name":"Mazuz-Harpaz"},{"first_name":"Kobi","last_name":"Cohen","full_name":"Cohen, Kobi"},{"first_name":"Klaus","last_name":"Biermann","full_name":"Biermann, Klaus"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"full_name":"West, Ken","last_name":"West","first_name":"Ken"},{"last_name":"Pfeiffer","first_name":"Loren","full_name":"Pfeiffer, Loren"},{"first_name":"Ronen","last_name":"Rapaport","full_name":"Rapaport, Ronen"},{"full_name":"Santos, Paulo","last_name":"Santos","first_name":"Paulo"}],"file":[{"date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T12:14:18Z","file_name":"2019_PhysReviewX_Hubert.pdf","relation":"main_file","checksum":"065ff82ee4a1d2c3773ce4b76ff4213c","access_level":"open_access","file_id":"6802","content_type":"application/pdf","creator":"dernst","file_size":1193550}],"has_accepted_license":"1","publisher":"American Physical Society"},{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"article_processing_charge":"Yes (via OA deal)","file":[{"date_created":"2019-08-12T12:05:58Z","date_updated":"2020-07-14T12:47:40Z","file_name":"2019_AnnalesHenriPoincare_Leopold.pdf","relation":"main_file","access_level":"open_access","checksum":"b6dbf0d837d809293d449adf77138904","file_size":681139,"creator":"dernst","file_id":"6801","content_type":"application/pdf"}],"title":"Mean-field dynamics for the Nelson model with fermions","author":[{"full_name":"Leopold, Nikolai K","last_name":"Leopold","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"last_name":"Petrat","orcid":"0000-0002-9166-5889","first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","has_accepted_license":"1","publication_status":"published","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","_id":"6788","file_date_updated":"2020-07-14T12:47:40Z","type":"journal_article","arxiv":1,"abstract":[{"lang":"eng","text":"We consider the Nelson model with ultraviolet cutoff, which describes the interaction between non-relativistic particles and a positive or zero mass quantized scalar field. We take the non-relativistic particles to obey Fermi statistics and discuss the time evolution in a mean-field limit of many fermions. In this case, the limit is known to be also a semiclassical limit. We prove convergence in terms of reduced density matrices of the many-body state to a tensor product of a Slater determinant with semiclassical structure and a coherent state, which evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations."}],"scopus_import":"1","publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"citation":{"chicago":"Leopold, Nikolai K, and Sören P Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” <i>Annales Henri Poincare</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00023-019-00828-w\">https://doi.org/10.1007/s00023-019-00828-w</a>.","ieee":"N. K. Leopold and S. P. Petrat, “Mean-field dynamics for the Nelson model with fermions,” <i>Annales Henri Poincare</i>, vol. 20, no. 10. Springer Nature, pp. 3471–3508, 2019.","short":"N.K. Leopold, S.P. Petrat, Annales Henri Poincare 20 (2019) 3471–3508.","ista":"Leopold NK, Petrat SP. 2019. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 20(10), 3471–3508.","ama":"Leopold NK, Petrat SP. Mean-field dynamics for the Nelson model with fermions. <i>Annales Henri Poincare</i>. 2019;20(10):3471–3508. doi:<a href=\"https://doi.org/10.1007/s00023-019-00828-w\">10.1007/s00023-019-00828-w</a>","mla":"Leopold, Nikolai K., and Sören P. Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” <i>Annales Henri Poincare</i>, vol. 20, no. 10, Springer Nature, 2019, pp. 3471–3508, doi:<a href=\"https://doi.org/10.1007/s00023-019-00828-w\">10.1007/s00023-019-00828-w</a>.","apa":"Leopold, N. K., &#38; Petrat, S. P. (2019). Mean-field dynamics for the Nelson model with fermions. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-019-00828-w\">https://doi.org/10.1007/s00023-019-00828-w</a>"},"year":"2019","external_id":{"isi":["000487036900008"],"arxiv":["1807.06781"]},"page":"3471–3508","issue":"10","oa":1,"date_updated":"2023-08-29T07:09:06Z","month":"10","intvolume":"        20","date_published":"2019-10-01T00:00:00Z","isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.1007/s00023-019-00828-w","publication":"Annales Henri Poincare","day":"01","status":"public","ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-08-11T21:59:21Z","volume":20},{"oa_version":"Preprint","ec_funded":1,"isi":1,"publication":"Bulletin of the London Mathematical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.04929"}],"doi":"10.1112/blms.12276","date_created":"2019-08-11T21:59:23Z","day":"01","status":"public","volume":51,"year":"2019","external_id":{"arxiv":["1903.04929"],"isi":["000478560200001"]},"page":"765-775","date_updated":"2023-08-29T07:08:34Z","oa":1,"issue":"5","date_published":"2019-10-01T00:00:00Z","month":"10","intvolume":"        51","project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"}],"publication_status":"published","_id":"6793","quality_controlled":"1","publication_identifier":{"eissn":["14692120"],"issn":["00246093"]},"citation":{"apa":"Akopyan, A., &#38; Izmestiev, I. (2019). The Regge symmetry, confocal conics, and the Schläfli formula. <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/blms.12276\">https://doi.org/10.1112/blms.12276</a>","mla":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” <i>Bulletin of the London Mathematical Society</i>, vol. 51, no. 5, London Mathematical Society, 2019, pp. 765–75, doi:<a href=\"https://doi.org/10.1112/blms.12276\">10.1112/blms.12276</a>.","ama":"Akopyan A, Izmestiev I. The Regge symmetry, confocal conics, and the Schläfli formula. <i>Bulletin of the London Mathematical Society</i>. 2019;51(5):765-775. doi:<a href=\"https://doi.org/10.1112/blms.12276\">10.1112/blms.12276</a>","ieee":"A. Akopyan and I. Izmestiev, “The Regge symmetry, confocal conics, and the Schläfli formula,” <i>Bulletin of the London Mathematical Society</i>, vol. 51, no. 5. London Mathematical Society, pp. 765–775, 2019.","ista":"Akopyan A, Izmestiev I. 2019. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 51(5), 765–775.","short":"A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51 (2019) 765–775.","chicago":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society, 2019. <a href=\"https://doi.org/10.1112/blms.12276\">https://doi.org/10.1112/blms.12276</a>."},"abstract":[{"text":"The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry.","lang":"eng"}],"scopus_import":"1","arxiv":1,"type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"HeEd"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"full_name":"Izmestiev, Ivan","last_name":"Izmestiev","first_name":"Ivan"}],"title":"The Regge symmetry, confocal conics, and the Schläfli formula","publisher":"London Mathematical Society"},{"page":"9597-9608","external_id":{"isi":["000479973400001"]},"year":"2019","month":"09","intvolume":"         9","date_published":"2019-09-01T00:00:00Z","date_updated":"2023-08-29T07:03:10Z","issue":"17","oa":1,"doi":"10.1002/ece3.5484","publication":"Ecology and Evolution","isi":1,"ec_funded":1,"oa_version":"Published Version","volume":9,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"date_created":"2019-08-11T21:59:24Z","day":"01","status":"public","article_processing_charge":"No","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Wiley","file":[{"file_name":"2019_EcologyEvolution_Trubenova.pdf","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:30:30Z","creator":"dernst","file_size":2839636,"content_type":"application/pdf","file_id":"6799","access_level":"open_access","checksum":"adcb70af4901977d95b8747eeee01bd7","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Green beards in the light of indirect genetic effects","author":[{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hager","first_name":"Reinmar","full_name":"Hager, Reinmar"}],"project":[{"call_identifier":"H2020","grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","name":"Rate of Adaptation in Changing Environment"}],"publication_status":"published","publication_identifier":{"eissn":["20457758"]},"citation":{"chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” <i>Ecology and Evolution</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/ece3.5484\">https://doi.org/10.1002/ece3.5484</a>.","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. <i>Ecology and Evolution</i>. 2019;9(17):9597-9608. doi:<a href=\"https://doi.org/10.1002/ece3.5484\">10.1002/ece3.5484</a>","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” <i>Ecology and Evolution</i>, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” <i>Ecology and Evolution</i>, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:<a href=\"https://doi.org/10.1002/ece3.5484\">10.1002/ece3.5484</a>.","apa":"Trubenova, B., &#38; Hager, R. (2019). Green beards in the light of indirect genetic effects. <i>Ecology and Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/ece3.5484\">https://doi.org/10.1002/ece3.5484</a>"},"type":"journal_article","file_date_updated":"2020-07-14T12:47:40Z","abstract":[{"lang":"eng","text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations."}],"scopus_import":"1","_id":"6795","quality_controlled":"1"},{"_id":"6818","quality_controlled":"1","publication_identifier":{"issn":["0143-7208"]},"citation":{"ama":"Yumusak C, Prochazkova AJ, Apaydin DH, et al. Indigoidine - Biosynthesized organic semiconductor. <i>Dyes and Pigments</i>. 2019;171. doi:<a href=\"https://doi.org/10.1016/j.dyepig.2019.107768\">10.1016/j.dyepig.2019.107768</a>","short":"C. Yumusak, A.J. Prochazkova, D.H. Apaydin, H. Seelajaroen, N.S. Sariciftci, M. Weiter, J. Krajcovic, Y. Qin, W. Zhang, J. Zhan, A. Kovalenko, Dyes and Pigments 171 (2019).","ista":"Yumusak C, Prochazkova AJ, Apaydin DH, Seelajaroen H, Sariciftci NS, Weiter M, Krajcovic J, Qin Y, Zhang W, Zhan J, Kovalenko A. 2019. Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. 171, 107768.","ieee":"C. Yumusak <i>et al.</i>, “Indigoidine - Biosynthesized organic semiconductor,” <i>Dyes and Pigments</i>, vol. 171. Elsevier, 2019.","chicago":"Yumusak, Cigdem, Anna Jancik Prochazkova, Dogukan H Apaydin, Hathaichanok Seelajaroen, Niyazi Serdar Sariciftci, Martin Weiter, Jozef Krajcovic, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” <i>Dyes and Pigments</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.dyepig.2019.107768\">https://doi.org/10.1016/j.dyepig.2019.107768</a>.","apa":"Yumusak, C., Prochazkova, A. J., Apaydin, D. H., Seelajaroen, H., Sariciftci, N. S., Weiter, M., … Kovalenko, A. (2019). Indigoidine - Biosynthesized organic semiconductor. <i>Dyes and Pigments</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dyepig.2019.107768\">https://doi.org/10.1016/j.dyepig.2019.107768</a>","mla":"Yumusak, Cigdem, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” <i>Dyes and Pigments</i>, vol. 171, 107768, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.dyepig.2019.107768\">10.1016/j.dyepig.2019.107768</a>."},"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Indigoidine is a blue natural pigment, which can be efficiently synthetized in E. coli. In addition to its antioxidant and antimicrobial activities indigoidine due to its stability and deep blue color can find an application as an industrial, environmentally friendly dye. Moreover, similarly to its counterpart regular indigo dye, due to its molecular structure, indigoidine is an organic semiconductor. Fully conjugated aromatic moiety and intermolecular hydrogen bonding of indigoidine result in an unusually narrow bandgap for such a small molecule. This, in its turn, result is tight molecular packing in the solid state and opens a path for a wide range of application in organic and bio-electronics, such as electrochemical and field effect transistors, organic solar cells, light and bio-sensors etc."}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Yumusak, Cigdem","first_name":"Cigdem","last_name":"Yumusak"},{"full_name":"Prochazkova, Anna Jancik","last_name":"Prochazkova","first_name":"Anna Jancik"},{"orcid":"0000-0002-1075-8857","last_name":"Apaydin","id":"2FF891BC-F248-11E8-B48F-1D18A9856A87","first_name":"Dogukan H","full_name":"Apaydin, Dogukan H"},{"first_name":"Hathaichanok","last_name":"Seelajaroen","full_name":"Seelajaroen, Hathaichanok"},{"full_name":"Sariciftci, Niyazi Serdar","last_name":"Sariciftci","first_name":"Niyazi Serdar"},{"full_name":"Weiter, Martin","last_name":"Weiter","first_name":"Martin"},{"full_name":"Krajcovic, Jozef","first_name":"Jozef","last_name":"Krajcovic"},{"last_name":"Qin","first_name":"Yong","full_name":"Qin, Yong"},{"last_name":"Zhang","first_name":"Wei","full_name":"Zhang, Wei"},{"full_name":"Zhan, Jixun","last_name":"Zhan","first_name":"Jixun"},{"last_name":"Kovalenko","first_name":"Alexander","full_name":"Kovalenko, Alexander"}],"title":"Indigoidine - Biosynthesized organic semiconductor","publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MaIb"}],"date_created":"2019-08-18T22:00:39Z","day":"01","status":"public","volume":171,"isi":1,"oa_version":"None","doi":"10.1016/j.dyepig.2019.107768","publication":"Dyes and Pigments","date_updated":"2023-08-29T07:11:09Z","month":"12","intvolume":"       171","date_published":"2019-12-01T00:00:00Z","article_number":"107768","year":"2019","external_id":{"isi":["000484870700099"]}},{"publication_status":"published","type":"journal_article","file_date_updated":"2020-07-14T12:47:40Z","scopus_import":1,"abstract":[{"text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.","lang":"eng"}],"publication_identifier":{"eissn":["1756-0500"]},"citation":{"chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” <i>BMC Research Notes</i>. BioMed Central, 2019. <a href=\"https://doi.org/10.1186/s13104-019-4534-3\">https://doi.org/10.1186/s13104-019-4534-3</a>.","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” <i>BMC Research Notes</i>, vol. 12. BioMed Central, 2019.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. <i>BMC Research Notes</i>. 2019;12. doi:<a href=\"https://doi.org/10.1186/s13104-019-4534-3\">10.1186/s13104-019-4534-3</a>","mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” <i>BMC Research Notes</i>, vol. 12, 494, BioMed Central, 2019, doi:<a href=\"https://doi.org/10.1186/s13104-019-4534-3\">10.1186/s13104-019-4534-3</a>.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., &#38; Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. <i>BMC Research Notes</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13104-019-4534-3\">https://doi.org/10.1186/s13104-019-4534-3</a>"},"quality_controlled":"1","_id":"6819","department":[{"_id":"LifeSc"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"BioMed Central","has_accepted_license":"1","file":[{"file_name":"2019_BMC_Antoniou.pdf","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-23T11:10:35Z","creator":"dernst","file_size":1177482,"content_type":"application/pdf","file_id":"6829","relation":"main_file","checksum":"4a2bb7994b7f2c432bf44f5127ea3102","access_level":"open_access"}],"author":[{"full_name":"Antoniou, Michael N.","last_name":"Antoniou","first_name":"Michael N."},{"full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mesnage, Robin","first_name":"Robin","last_name":"Mesnage"},{"last_name":"Biserni","first_name":"Martina","full_name":"Biserni, Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"last_name":"Martin","first_name":"Cristina Vazquez","full_name":"Martin, Cristina Vazquez"}],"title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1186/s13104-019-4534-3","publication":"BMC Research Notes","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9784"}]},"pmid":1,"volume":12,"status":"public","day":"08","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2019-08-18T22:00:39Z","external_id":{"pmid":["31395095"]},"year":"2019","article_number":"494","intvolume":"        12","month":"08","date_published":"2019-08-08T00:00:00Z","oa":1,"date_updated":"2023-02-23T14:08:14Z"},{"date_published":"2019-11-01T00:00:00Z","month":"11","intvolume":"        19","oa":1,"issue":"6","date_updated":"2023-08-29T07:10:44Z","page":"1447-1460","external_id":{"isi":["000480196800001"],"pmid":["31325910"]},"year":"2019","volume":19,"pmid":1,"status":"public","day":"01","date_created":"2019-08-18T22:00:41Z","publication":"Molecular Ecology Resources","doi":"10.1111/1755-0998.13062","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727"}],"oa_version":"Submitted Version","isi":1,"publisher":"Wiley","author":[{"full_name":"Yourick, Miranda R.","last_name":"Yourick","first_name":"Miranda R."},{"last_name":"Sandkam","first_name":"Benjamin A.","full_name":"Sandkam, Benjamin A."},{"full_name":"Gammerdinger, William J","first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","last_name":"Gammerdinger"},{"full_name":"Escobar-Camacho, Daniel","last_name":"Escobar-Camacho","first_name":"Daniel"},{"full_name":"Nandamuri, Sri Pratima","first_name":"Sri Pratima","last_name":"Nandamuri"},{"last_name":"Clark","first_name":"Frances E.","full_name":"Clark, Frances E."},{"last_name":"Joyce","first_name":"Brendan","full_name":"Joyce, Brendan"},{"first_name":"Matthew A.","last_name":"Conte","full_name":"Conte, Matthew A."},{"last_name":"Kocher","first_name":"Thomas D.","full_name":"Kocher, Thomas D."},{"first_name":"Karen L.","last_name":"Carleton","full_name":"Carleton, Karen L."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses","department":[{"_id":"BeVi"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined."}],"scopus_import":"1","type":"journal_article","citation":{"mla":"Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” <i>Molecular Ecology Resources</i>, vol. 19, no. 6, Wiley, 2019, pp. 1447–60, doi:<a href=\"https://doi.org/10.1111/1755-0998.13062\">10.1111/1755-0998.13062</a>.","apa":"Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri, S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13062\">https://doi.org/10.1111/1755-0998.13062</a>","chicago":"Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” <i>Molecular Ecology Resources</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/1755-0998.13062\">https://doi.org/10.1111/1755-0998.13062</a>.","ama":"Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. <i>Molecular Ecology Resources</i>. 2019;19(6):1447-1460. doi:<a href=\"https://doi.org/10.1111/1755-0998.13062\">10.1111/1755-0998.13062</a>","ista":"Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 19(6), 1447–1460.","short":"M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri, F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology Resources 19 (2019) 1447–1460.","ieee":"M. R. Yourick <i>et al.</i>, “Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses,” <i>Molecular Ecology Resources</i>, vol. 19, no. 6. Wiley, pp. 1447–1460, 2019."},"publication_identifier":{"eissn":["1755-0998"]},"quality_controlled":"1","_id":"6821","publication_status":"published"},{"publication_status":"published","project":[{"_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"quality_controlled":"1","_id":"6822","scopus_import":1,"abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher\r\nbidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called \r\n randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one."}],"type":"conference","file_date_updated":"2020-07-14T12:47:41Z","publication_identifier":{"isbn":["978-303030805-6"],"issn":["0302-9743"]},"citation":{"mla":"Avni, Guy, et al. “Bidding Games on Markov Decision Processes.” <i> Proceedings of the 13th International Conference of Reachability Problems</i>, vol. 11674, Springer, 2019, pp. 1–12, doi:<a href=\"https://doi.org/10.1007/978-3-030-30806-3_1\">10.1007/978-3-030-30806-3_1</a>.","apa":"Avni, G., Henzinger, T. A., Ibsen-Jensen, R., &#38; Novotny, P. (2019). Bidding games on Markov decision processes. In <i> Proceedings of the 13th International Conference of Reachability Problems</i> (Vol. 11674, pp. 1–12). Brussels, Belgium: Springer. <a href=\"https://doi.org/10.1007/978-3-030-30806-3_1\">https://doi.org/10.1007/978-3-030-30806-3_1</a>","chicago":"Avni, Guy, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Petr Novotny. “Bidding Games on Markov Decision Processes.” In <i> Proceedings of the 13th International Conference of Reachability Problems</i>, 11674:1–12. Springer, 2019. <a href=\"https://doi.org/10.1007/978-3-030-30806-3_1\">https://doi.org/10.1007/978-3-030-30806-3_1</a>.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, P. Novotny, in:,  Proceedings of the 13th International Conference of Reachability Problems, Springer, 2019, pp. 1–12.","ista":"Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. 2019. Bidding games on Markov decision processes.  Proceedings of the 13th International Conference of Reachability Problems. RP: Reachability Problems, LNCS, vol. 11674, 1–12.","ieee":"G. Avni, T. A. Henzinger, R. Ibsen-Jensen, and P. Novotny, “Bidding games on Markov decision processes,” in <i> Proceedings of the 13th International Conference of Reachability Problems</i>, Brussels, Belgium, 2019, vol. 11674, pp. 1–12.","ama":"Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. Bidding games on Markov decision processes. In: <i> Proceedings of the 13th International Conference of Reachability Problems</i>. Vol 11674. Springer; 2019:1-12. doi:<a href=\"https://doi.org/10.1007/978-3-030-30806-3_1\">10.1007/978-3-030-30806-3_1</a>"},"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"title":"Bidding games on Markov decision processes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"last_name":"Novotny","first_name":"Petr","full_name":"Novotny, Petr"}],"file":[{"relation":"main_file","checksum":"45ebbc709af2b247d28c7c293c01504b","access_level":"open_access","content_type":"application/pdf","file_id":"6823","creator":"gavni","file_size":436635,"date_created":"2019-08-19T07:56:40Z","date_updated":"2020-07-14T12:47:41Z","file_name":"prob.pdf"}],"publisher":"Springer","has_accepted_license":"1","oa_version":"Submitted Version","publication":" Proceedings of the 13th International Conference of Reachability Problems","doi":"10.1007/978-3-030-30806-3_1","status":"public","day":"06","ddc":["000"],"date_created":"2019-08-19T07:58:10Z","volume":11674,"year":"2019","conference":{"end_date":"2019-09-13","start_date":"2019-09-11","name":"RP: Reachability Problems","location":"Brussels, Belgium"},"page":"1-12","oa":1,"date_updated":"2021-01-12T08:09:12Z","date_published":"2019-09-06T00:00:00Z","alternative_title":["LNCS"],"month":"09","intvolume":"     11674"},{"citation":{"ieee":"F. R. Gärtner and S. Massberg, “Patrolling the vascular borders: Platelets in immunity to infection and cancer,” <i>Nature Reviews Immunology</i>, vol. 19, no. 12. Springer Nature, pp. 747–760, 2019.","short":"F.R. Gärtner, S. Massberg, Nature Reviews Immunology 19 (2019) 747–760.","ista":"Gärtner FR, Massberg S. 2019. Patrolling the vascular borders: Platelets in immunity to infection and cancer. Nature Reviews Immunology. 19(12), 747–760.","ama":"Gärtner FR, Massberg S. Patrolling the vascular borders: Platelets in immunity to infection and cancer. <i>Nature Reviews Immunology</i>. 2019;19(12):747–760. doi:<a href=\"https://doi.org/10.1038/s41577-019-0202-z\">10.1038/s41577-019-0202-z</a>","chicago":"Gärtner, Florian R, and Steffen Massberg. “Patrolling the Vascular Borders: Platelets in Immunity to Infection and Cancer.” <i>Nature Reviews Immunology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41577-019-0202-z\">https://doi.org/10.1038/s41577-019-0202-z</a>.","apa":"Gärtner, F. R., &#38; Massberg, S. (2019). Patrolling the vascular borders: Platelets in immunity to infection and cancer. <i>Nature Reviews Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41577-019-0202-z\">https://doi.org/10.1038/s41577-019-0202-z</a>","mla":"Gärtner, Florian R., and Steffen Massberg. “Patrolling the Vascular Borders: Platelets in Immunity to Infection and Cancer.” <i>Nature Reviews Immunology</i>, vol. 19, no. 12, Springer Nature, 2019, pp. 747–760, doi:<a href=\"https://doi.org/10.1038/s41577-019-0202-z\">10.1038/s41577-019-0202-z</a>."},"publication_identifier":{"eissn":["1474-1741"],"issn":["1474-1733"]},"type":"journal_article","abstract":[{"text":"Platelets are small anucleate cellular fragments that are released by megakaryocytes and safeguard vascular integrity through a process termed ‘haemostasis’. However, platelets have important roles beyond haemostasis as they contribute to the initiation and coordination of intravascular immune responses. They continuously monitor blood vessel integrity and tightly coordinate vascular trafficking and functions of multiple cell types. In this way platelets act as ‘patrolling officers of the vascular highway’ that help to establish effective immune responses to infections and cancer. Here we discuss the distinct biological features of platelets that allow them to shape immune responses to pathogens and tumour cells, highlighting the parallels between these responses.","lang":"eng"}],"scopus_import":"1","_id":"6824","quality_controlled":"1","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","call_identifier":"H2020"}],"publication_status":"published","publisher":"Springer Nature","author":[{"last_name":"Gärtner","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","full_name":"Gärtner, Florian R"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"}],"title":"Patrolling the vascular borders: Platelets in immunity to infection and cancer","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"article_type":"original","pmid":1,"volume":19,"date_created":"2019-08-20T17:24:32Z","status":"public","day":"01","doi":"10.1038/s41577-019-0202-z","publication":"Nature Reviews Immunology","isi":1,"ec_funded":1,"oa_version":"None","month":"12","intvolume":"        19","date_published":"2019-12-01T00:00:00Z","date_updated":"2023-08-29T07:16:14Z","issue":"12","page":"747–760","external_id":{"isi":["000499090600011"],"pmid":["31409920"]},"year":"2019"},{"department":[{"_id":"JoCs"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The hippocampus and medial prefrontal cortex during flexible behavior","author":[{"full_name":"Käfer, Karola","last_name":"Käfer","first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2019-09-03T08:07:13Z","date_updated":"2020-09-06T22:30:03Z","file_name":"Thesis_Kaefer_PDFA.pdf","request_a_copy":0,"embargo":"2020-09-05","checksum":"2664420e332a33338568f4f3bfc59287","access_level":"open_access","relation":"main_file","file_size":3205202,"creator":"kkaefer","content_type":"application/pdf","file_id":"6846"},{"file_id":"6847","content_type":"application/zip","creator":"kkaefer","file_size":2506835,"embargo_to":"open_access","relation":"main_file","checksum":"9a154eab6f07aa590a3d2651dc0d926a","access_level":"closed","file_name":"Thesis_Kaefer.zip","date_created":"2019-09-03T08:07:17Z","date_updated":"2020-09-15T22:30:05Z"}],"publication_status":"published","abstract":[{"text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. ","lang":"eng"}],"type":"dissertation","file_date_updated":"2020-09-15T22:30:05Z","citation":{"mla":"Käfer, Karola. <i>The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>.","apa":"Käfer, K. (2019). <i>The hippocampus and medial prefrontal cortex during flexible behavior</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>.","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria."},"publication_identifier":{"issn":["2663-337X"]},"_id":"6825","page":"89","year":"2019","alternative_title":["ISTA Thesis"],"date_published":"2019-08-24T00:00:00Z","month":"08","oa":1,"date_updated":"2023-09-07T13:01:42Z","doi":"10.15479/AT:ISTA:6825","degree_awarded":"PhD","oa_version":"Published Version","related_material":{"record":[{"id":"5949","relation":"part_of_dissertation","status":"public"}]},"day":"24","status":"public","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"date_created":"2019-08-21T15:00:57Z","ddc":["570"]}]