[{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"day":"01","status":"public","year":"2018","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"09","external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","volume":17,"oa":1,"isi":1,"publication":"Briefings in Functional Genomics","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"doi":"10.1093/bfgp/ely007","publication_identifier":{"issn":["2041-2649"],"eissn":["2041-2657"]},"type":"journal_article","intvolume":"        17","date_updated":"2023-09-19T15:11:22Z","abstract":[{"lang":"eng","text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation."}],"page":"329-338","article_type":"original","issue":"5","author":[{"id":"4968E7C8-F248-11E8-B48F-1D18A9856A87","last_name":"Yuuta","orcid":"0000-0002-2853-8051","full_name":"Yuuta, Moriyama","first_name":"Moriyama"},{"full_name":"Koshiba-Takeuchi, Kazuko","first_name":"Kazuko","last_name":"Koshiba-Takeuchi"}],"acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bfgp/ely007"}],"date_created":"2022-03-18T12:40:35Z","citation":{"short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>.","apa":"Yuuta, M., &#38; Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. 2018;17(5):329-338. doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338."},"publication_status":"published","date_published":"2018-09-01T00:00:00Z","_id":"10880","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","department":[{"_id":"CaHe"}],"publisher":"Oxford University Press"},{"date_created":"2022-03-18T12:43:22Z","publication_status":"published","citation":{"apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378. doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>.","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378."},"_id":"10881","date_published":"2018-04-13T00:00:00Z","ec_funded":1,"title":"Molecular evolution and diversification of the SMXL gene family","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"type":"journal_article","intvolume":"        69","date_updated":"2025-05-07T11:12:33Z","page":"2367-2378","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}],"article_type":"original","issue":"9","acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","author":[{"last_name":"Moturu","first_name":"Taraka Ramji","full_name":"Moturu, Taraka Ramji"},{"last_name":"Thula","first_name":"Sravankumar","full_name":"Thula, Sravankumar"},{"full_name":"Singh, Ravi Kumar","first_name":"Ravi Kumar","last_name":"Singh"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková"},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu"}],"volume":69,"isi":1,"publication":"Journal of Experimental Botany","keyword":["Plant Science","Physiology"],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"doi":"10.1093/jxb/ery097","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"day":"13","language":[{"iso":"eng"}],"year":"2018","status":"public","article_processing_charge":"No","month":"04","external_id":{"pmid":["29538714"],"isi":["000430727000016"]},"quality_controlled":"1","scopus_import":"1","oa_version":"None"},{"type":"conference","publication_identifier":{"isbn":["9781538664209"],"eissn":["2575-7075"]},"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"author":[{"last_name":"Uijlings","first_name":"Jasper","full_name":"Uijlings, Jasper"},{"last_name":"Konyushkova","full_name":"Konyushkova, Ksenia","first_name":"Ksenia"},{"first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"},{"last_name":"Ferrari","first_name":"Vittorio","full_name":"Ferrari, Vittorio"}],"conference":{"start_date":"2018-06-18","end_date":"2018-06-23","location":"Salt Lake City, UT, United States","name":"CVF: Conference on Computer Vision and Pattern Recognition"},"abstract":[{"lang":"eng","text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger."}],"page":"9175-9184","date_updated":"2023-09-19T15:11:49Z","title":"Learning intelligent dialogs for bounding box annotation","date_published":"2018-12-17T00:00:00Z","_id":"10882","citation":{"ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 9175–84. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 9175–84, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>.","apa":"Uijlings, J., Konyushkova, K., Lampert, C., &#38; Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:9175-9184. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, United States, 2018, pp. 9175–9184."},"publication_status":"published","date_created":"2022-03-18T12:45:09Z","publisher":"IEEE","department":[{"_id":"ChLa"}],"month":"12","article_processing_charge":"No","year":"2018","language":[{"iso":"eng"}],"status":"public","day":"17","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","quality_controlled":"1","external_id":{"arxiv":["1712.08087"],"isi":["000457843609036"]},"oa":1,"doi":"10.1109/cvpr.2018.00956","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","arxiv":1,"isi":1},{"quality_controlled":"1","external_id":{"arxiv":["1909.04983"]},"has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","day":"23","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","alternative_title":["EPiC Series in Computing"],"month":"10","article_processing_charge":"No","status":"public","year":"2018","language":[{"iso":"eng"}],"publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","arxiv":1,"doi":"10.29007/5z5k","project":[{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"oa":1,"volume":57,"conference":{"end_date":"2018-11-21","start_date":"2018-11-17","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","location":"Awassa, Ethiopia"},"page":"233-253","abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"date_updated":"2022-07-29T09:24:31Z","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Dvořák","first_name":"Wolfgang","full_name":"Dvořák, Wolfgang"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Alexander","full_name":"Svozil, Alexander","last_name":"Svozil"}],"file_date_updated":"2022-05-17T07:51:08Z","ddc":["000"],"publication_identifier":{"issn":["2398-7340"]},"intvolume":"        57","type":"conference","file":[{"content_type":"application/pdf","file_name":"2018_EPiCs_Chatterjee.pdf","date_created":"2022-05-17T07:51:08Z","creator":"dernst","file_size":720893,"success":1,"file_id":"11392","date_updated":"2022-05-17T07:51:08Z","checksum":"1229aa8640bd6db610c85decf2265480","relation":"main_file","access_level":"open_access"}],"publisher":"EasyChair","department":[{"_id":"KrCh"}],"citation":{"ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, 57:233–53. EasyChair, 2018. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, vol. 57, EasyChair, 2018, pp. 233–53, doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., &#38; Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i> (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>. Vol 57. EasyChair; 2018:233-253. doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>"},"publication_status":"published","date_created":"2022-03-18T12:46:32Z","ec_funded":1,"title":"Quasipolynomial set-based symbolic algorithms for parity games","date_published":"2018-10-23T00:00:00Z","_id":"10883"},{"intvolume":"       270","type":"conference","date_updated":"2021-01-12T06:48:16Z","conference":{"location":"Munich, Germany","name":"MaLiQS: Macroscopic Limits of Quantum Systems","start_date":"2017-03-30","end_date":"2017-04-01"},"abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"page":"185 - 214","author":[{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","last_name":"Leopold","first_name":"Nikolai K","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822"},{"first_name":"Peter","full_name":"Pickl, Peter","last_name":"Pickl"}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"citation":{"ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>","apa":"Leopold, N. K., &#38; Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>","mla":"Leopold, Nikolai K., and Peter Pickl. <i>Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields</i>. Vol. 270, Springer, 2018, pp. 185–214, doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214."},"publication_status":"published","date_created":"2018-12-11T11:44:08Z","date_published":"2018-10-27T00:00:00Z","_id":"11","ec_funded":1,"title":"Mean-field limits of particles in interaction with quantised radiation fields","publisher":"Springer","department":[{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"8045","day":"27","year":"2018","language":[{"iso":"eng"}],"status":"public","month":"10","external_id":{"arxiv":["1806.10843"]},"quality_controlled":"1","scopus_import":1,"oa_version":"Preprint","oa":1,"volume":270,"arxiv":1,"doi":"10.1007/978-3-030-01602-9_9","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"}]},{"volume":37,"oa":1,"project":[{"grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"},{"name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020"}],"doi":"10.1145/3197517.3201341","isi":1,"publication":"ACM Transaction on Graphics","language":[{"iso":"eng"}],"status":"public","year":"2018","article_processing_charge":"No","month":"08","publist_id":"8044","pubrep_id":"1037","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"04","scopus_import":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/"}]},"oa_version":"Submitted Version","has_accepted_license":"1","external_id":{"isi":["000448185000096"]},"quality_controlled":"1","_id":"12","date_published":"2018-08-04T00:00:00Z","ec_funded":1,"title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","date_created":"2018-12-11T11:44:09Z","citation":{"apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., &#38; Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4. ACM, 2018.","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>.","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4, 135, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>.","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135."},"publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"ACM","file":[{"file_size":104225664,"file_id":"5360","creator":"system","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","date_created":"2018-12-12T10:18:38Z"},{"date_updated":"2020-07-14T12:44:38Z","checksum":"3861e693ba47c51f3ec7b7867d573a61","access_level":"open_access","relation":"main_file","file_size":377743553,"file_id":"5361","creator":"system","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","date_created":"2018-12-12T10:18:39Z","content_type":"application/zip"},{"content_type":"video/vnd.objectvideo","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","date_created":"2018-12-12T10:18:41Z","file_id":"5362","file_size":162634396,"creator":"system","checksum":"490040c685ed869536e2a18f5a906b94","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","relation":"main_file"},{"file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","date_created":"2018-12-12T10:18:42Z","content_type":"image/jpeg","checksum":"be7fc8b229adda727419b6504b3b9352","date_updated":"2020-07-14T12:44:38Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5363","file_size":527972}],"intvolume":"        37","type":"journal_article","ddc":["004","516","670"],"file_date_updated":"2020-07-14T12:44:38Z","issue":"4","author":[{"first_name":"Kazutaka","full_name":"Nakashima, Kazutaka","last_name":"Nakashima"},{"orcid":"0000-0002-1546-3265","first_name":"Thomas","full_name":"Auzinger, Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emmanuel","full_name":"Iarussi, Emmanuel","last_name":"Iarussi","id":"33F19F16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3808-281X","first_name":"Ran","full_name":"Zhang, Ran"},{"full_name":"Igarashi, Takeo","first_name":"Takeo","last_name":"Igarashi"},{"first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-11T12:48:09Z","article_number":"135","abstract":[{"lang":"eng","text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects."}]},{"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"type":"journal_article","intvolume":"        50","date_updated":"2023-10-18T07:21:53Z","article_type":"original","page":"130-137","abstract":[{"text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.","lang":"eng"}],"issue":"1","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","author":[{"first_name":"James","full_name":"Walker, James","last_name":"Walker"},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"last_name":"Zhang","first_name":"Jingyi","full_name":"Zhang, Jingyi"},{"last_name":"Aldridge","full_name":"Aldridge, Billy","first_name":"Billy"},{"last_name":"Vickers","full_name":"Vickers, Martin","first_name":"Martin"},{"last_name":"Higgins","first_name":"James D.","full_name":"Higgins, James D."},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}],"date_created":"2023-01-16T09:18:05Z","publication_status":"published","citation":{"short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137."},"date_published":"2017-12-18T00:00:00Z","_id":"12193","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","department":[{"_id":"XiFe"}],"publisher":"Nature Research","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"day":"18","year":"2017","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","month":"12","external_id":{"pmid":["29255257"]},"quality_controlled":"1","scopus_import":"1","oa_version":"None","volume":50,"oa":1,"publication":"Nature Genetics","keyword":["Genetics"],"doi":"10.1038/s41588-017-0008-5"},{"file":[{"date_created":"2018-12-12T10:10:48Z","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:39Z","checksum":"c572cf02be8fbb7020cfcfb892182e4c","file_id":"4838","file_size":169145,"creator":"system"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"GaNo"}],"publisher":"Wiley-Blackwell","date_created":"2018-12-11T11:50:50Z","citation":{"ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>.","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>.","apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>"},"publication_status":"published","date_published":"2017-01-01T00:00:00Z","_id":"1228","title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","date_updated":"2023-09-20T11:16:01Z","abstract":[{"text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.","lang":"eng"}],"article_type":"review","page":"45 - 57","file_date_updated":"2020-07-14T12:44:39Z","issue":"1","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","author":[{"last_name":"Sauerzopf","full_name":"Sauerzopf, Ulrich","first_name":"Ulrich"},{"id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","last_name":"Sacco","full_name":"Sacco, Roberto","first_name":"Roberto"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia"},{"last_name":"Niello","first_name":"Marco","full_name":"Niello, Marco"},{"last_name":"Weidenauer","full_name":"Weidenauer, Ana","first_name":"Ana"},{"first_name":"Nicole","full_name":"Praschak Rieder, Nicole","last_name":"Praschak Rieder"},{"full_name":"Sitte, Harald","first_name":"Harald","last_name":"Sitte"},{"last_name":"Willeit","full_name":"Willeit, Matthaeus","first_name":"Matthaeus"}],"ddc":["616"],"type":"journal_article","intvolume":"        45","isi":1,"publication":"European Journal of Neuroscience","doi":"10.1111/ejn.13418","volume":45,"oa":1,"has_accepted_license":"1","external_id":{"pmid":["27690184"],"isi":["000392487100005"]},"quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","publist_id":"6106","pubrep_id":"738","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"day":"01","year":"2017","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","month":"01"},{"date_created":"2018-12-11T11:51:12Z","publication_status":"published","citation":{"ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170."},"title":"Trading performance for stability in Markov decision processes","ec_funded":1,"_id":"1294","date_published":"2017-03-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:44:42Z","checksum":"91271b23cf884d7c06d33bef0cd623b1","relation":"main_file","access_level":"open_access","creator":"system","file_size":708657,"file_id":"4885","file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","date_created":"2018-12-12T10:11:30Z","content_type":"application/pdf"}],"department":[{"_id":"KrCh"}],"publisher":"Elsevier","ddc":["004","006"],"type":"journal_article","intvolume":"        84","abstract":[{"lang":"eng","text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints."}],"page":"144 - 170","date_updated":"2023-09-20T11:15:31Z","author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"}],"file_date_updated":"2020-07-14T12:44:42Z","volume":84,"oa":1,"publication":"Journal of Computer and System Sciences","isi":1,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"doi":"10.1016/j.jcss.2016.09.009","day":"01","publist_id":"6009","pubrep_id":"717","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"03","status":"public","year":"2017","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","has_accepted_license":"1","external_id":{"isi":["000388430000011"]},"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"2305","relation":"earlier_version"}]},"scopus_import":"1"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1701.05738"}],"author":[{"full_name":"Kretinsky, Jan","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","first_name":"Tobias","full_name":"Meggendorfer, Tobias"},{"first_name":"Clara","full_name":"Waldmann, Clara","last_name":"Waldmann"},{"first_name":"Maximilian","full_name":"Weininger, Maximilian","last_name":"Weininger"}],"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","date_updated":"2023-06-21T13:29:46Z","abstract":[{"text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.","lang":"eng"}],"page":"443-460","conference":{"start_date":"2017-04-22","end_date":"2017-04-29","location":"Uppsala, Sweden","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"type":"conference","intvolume":"     10205","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662545768"],"eissn":["1611-3349"],"eisbn":["9783662545775"]},"department":[{"_id":"KrCh"}],"publisher":"Springer","date_published":"2017-03-31T00:00:00Z","_id":"13160","title":"Index appearance record for transforming Rabin automata into parity automata","date_created":"2023-06-21T13:21:14Z","publication_status":"published","citation":{"short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460."},"oa_version":"Preprint","external_id":{"arxiv":["1701.05738"]},"quality_controlled":"1","status":"public","year":"2017","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"03","alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"31","doi":"10.1007/978-3-662-54577-5_26","arxiv":1,"publication":"Tools and Algorithms for the Construction and Analysis of Systems","volume":10205,"oa":1},{"month":"08","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"year":"2017","day":"25","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6829","pubrep_id":"857","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","has_accepted_license":"1","oa":1,"supervisor":[{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:th_857","project":[{"call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"type":"dissertation","ddc":["576","577","579"],"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","author":[{"last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","full_name":"Jesse, Fabienne","first_name":"Fabienne"}],"file_date_updated":"2020-07-14T12:48:10Z","abstract":[{"text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.","lang":"eng"}],"page":"87","date_updated":"2023-09-07T12:01:21Z","title":"The lac operon in the wild","ec_funded":1,"_id":"820","date_published":"2017-08-25T00:00:00Z","citation":{"ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","apa":"Jesse, F. (2017). <i>The lac operon in the wild</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","ama":"Jesse F. The lac operon in the wild. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>.","mla":"Jesse, Fabienne. <i>The Lac Operon in the Wild</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>."},"publication_status":"published","date_created":"2018-12-11T11:48:41Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoBo"}],"degree_awarded":"PhD","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:17:00Z","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","creator":"system","file_id":"5252","file_size":3417773,"relation":"main_file","access_level":"open_access","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","date_updated":"2020-07-14T12:48:10Z"},{"creator":"dernst","file_size":215899,"file_id":"6212","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","date_updated":"2020-07-14T12:48:10Z","relation":"source_file","access_level":"closed","content_type":"application/x-tex","file_name":"2017_thesis_Jesse_source.tex","date_created":"2019-04-05T08:51:59Z"}]},{"citation":{"ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","mla":"Pavlogiannis, Andreas. <i>Algorithmic Advances in Program Analysis and Their Applications</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>.","chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>.","apa":"Pavlogiannis, A. (2017). <i>Algorithmic advances in program analysis and their applications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017."},"publication_status":"published","date_created":"2018-12-11T11:48:41Z","date_published":"2017-08-09T00:00:00Z","_id":"821","title":"Algorithmic advances in program analysis and their applications","ec_funded":1,"file":[{"checksum":"3a3ec003f6ee73f41f82a544d63dfc77","date_updated":"2020-07-14T12:48:10Z","relation":"main_file","access_level":"open_access","creator":"system","file_size":4103115,"file_id":"4900","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","date_created":"2018-12-12T10:11:44Z","content_type":"application/pdf"},{"date_updated":"2020-07-14T12:48:10Z","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","relation":"source_file","access_level":"closed","creator":"dernst","file_id":"6201","file_size":14744374,"file_name":"2017_thesis_Pavlogiannis.zip","date_created":"2019-04-05T07:59:31Z","content_type":"application/zip"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png"},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"}],"publication_identifier":{"issn":["2663-337X"]},"ddc":["000"],"type":"dissertation","date_updated":"2023-09-07T12:01:59Z","page":"418","abstract":[{"text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between  traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method  called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:10Z","author":[{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here.  I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta,  Arjun Radhakrishna,  Petr Novontý,  Christian Hilbe,  Jakob Ruess,  Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey.  Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","oa":1,"supervisor":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"}],"doi":"10.15479/AT:ISTA:th_854","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6828","alternative_title":["ISTA Thesis"],"pubrep_id":"854","day":"09","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"year":"2017","month":"08","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1071"},{"relation":"part_of_dissertation","id":"1437","status":"public"},{"status":"public","id":"1602","relation":"part_of_dissertation"},{"status":"public","id":"1604","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1607"},{"id":"1714","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version"},{"publication_identifier":{"issn":["00278424"]},"intvolume":"       114","type":"journal_article","abstract":[{"lang":"eng","text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. "}],"page":"10666 - 10671","date_updated":"2023-09-26T16:18:48Z","author":[{"full_name":"De Vos, Marjon","first_name":"Marjon","last_name":"De Vos","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","first_name":"Marcin P","orcid":"0000-0001-7896-7762"},{"full_name":"Mcnally, Alan","first_name":"Alan","last_name":"Mcnally"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/","open_access":"1"}],"issue":"40","citation":{"ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” <i>PNAS</i>, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. 2017;114(40):10666-10671. doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., &#38; Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>.","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671."},"publication_status":"published","date_created":"2018-12-11T11:48:41Z","ec_funded":1,"title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","date_published":"2017-10-03T00:00:00Z","_id":"822","publisher":"National Academy of Sciences","department":[{"_id":"ToBo"}],"day":"03","pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6827","month":"10","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2017","status":"public","quality_controlled":"1","external_id":{"isi":["000412130500061"],"pmid":["28923953"]},"oa_version":"Submitted Version","scopus_import":"1","oa":1,"volume":114,"publication":"PNAS","isi":1,"doi":"10.1073/pnas.1713372114","project":[{"name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"}]},{"type":"journal_article","intvolume":"      2017","publication_identifier":{"issn":["17425468"]},"issue":"9","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.06303"}],"author":[{"full_name":"Colabrese, Simona","first_name":"Simona","last_name":"Colabrese"},{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele"},{"first_name":"Luca","full_name":"Leuzzi, Luca","last_name":"Leuzzi"},{"full_name":"Marinari, Enzo","first_name":"Enzo","last_name":"Marinari"}],"date_updated":"2023-09-26T16:18:12Z","article_number":"093404","abstract":[{"lang":"eng","text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region."}],"_id":"823","date_published":"2017-09-26T00:00:00Z","ec_funded":1,"title":"Phase transitions in integer linear problems","date_created":"2018-12-11T11:48:41Z","citation":{"ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems.  Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience, 2017. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>.","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>.","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari,  Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9. IOPscience, 2017.","ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. 2017;2017(9). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>","apa":"Colabrese, S., De Martino, D., Leuzzi, L., &#38; Marinari, E. (2017). Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>"},"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"IOPscience","year":"2017","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","month":"09","publist_id":"6826","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"26","scopus_import":"1","oa_version":"Submitted Version","external_id":{"isi":["000411842900001"]},"quality_controlled":"1","volume":2017,"oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"doi":"10.1088/1742-5468/aa85c3","isi":1,"publication":" Journal of Statistical Mechanics: Theory and Experiment"},{"publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"publication_status":"published","citation":{"ista":"Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1.","apa":"Budanur, N. B., &#38; Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>","ama":"Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;827. doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>","ieee":"N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 827. Cambridge University Press, 2017.","short":"N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).","chicago":"Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>.","mla":"Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 827, R1, Cambridge University Press, 2017, doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>."},"date_created":"2018-12-11T11:48:42Z","title":"Heteroclinic path to spatially localized chaos in pipe flow","date_published":"2017-08-18T00:00:00Z","_id":"824","article_number":"R1","abstract":[{"text":"In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff.","lang":"eng"}],"date_updated":"2023-09-26T16:17:43Z","author":[{"last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","orcid":"0000-0003-0423-5010"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.10484"}],"publication_identifier":{"issn":["00221120"]},"intvolume":"       827","type":"journal_article","publication":"Journal of Fluid Mechanics","isi":1,"doi":"10.1017/jfm.2017.516","oa":1,"volume":827,"quality_controlled":"1","external_id":{"isi":["000408326300001"]},"oa_version":"Submitted Version","scopus_import":"1","day":"18","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6824","month":"08","article_processing_charge":"No","year":"2017","language":[{"iso":"eng"}],"status":"public"},{"conference":{"start_date":"2017-08-22","end_date":"2017-08-24","name":"CAIP: Computer Analysis of Images and Patterns","location":"Ystad, Sweden"},"abstract":[{"text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams.","lang":"eng"}],"page":"397 - 409","date_updated":"2023-09-26T16:10:03Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02045"}],"author":[{"orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","first_name":"Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss"},{"last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","first_name":"Hubert"}],"publication_identifier":{"issn":["03029743"]},"editor":[{"last_name":"Felsberg","full_name":"Felsberg, Michael","first_name":"Michael"},{"last_name":"Heyden","full_name":"Heyden, Anders","first_name":"Anders"},{"last_name":"Krüger","first_name":"Norbert","full_name":"Krüger, Norbert"}],"type":"conference","intvolume":"     10424","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","citation":{"ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","apa":"Heiss, T., &#38; Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, &#38; N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.","ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409.","mla":"Heiss, Teresa, and Hubert Wagner. <i>Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images</i>. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>.","chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>."},"date_created":"2018-12-11T11:48:45Z","title":"Streaming algorithm for Euler characteristic curves of multidimensional images","date_published":"2017-07-28T00:00:00Z","_id":"833","quality_controlled":"1","external_id":{"isi":["000432085900032"]},"oa_version":"Submitted Version","scopus_import":"1","day":"28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"publist_id":"6815","month":"07","article_processing_charge":"No","year":"2017","language":[{"iso":"eng"}],"status":"public","isi":1,"doi":"10.1007/978-3-319-64689-3_32","oa":1,"volume":10424},{"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","year":"2017","month":"09","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6814","day":"06","scopus_import":"1","oa_version":"Submitted Version","external_id":{"isi":["000409429300004"]},"quality_controlled":"1","oa":1,"volume":96,"doi":"10.1103/PhysRevB.96.104201","isi":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","type":"journal_article","intvolume":"        96","publication_identifier":{"issn":["24699950"]},"issue":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02389"}],"author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"last_name":"Zlatko","first_name":"Papic","full_name":"Zlatko, Papic"},{"last_name":"Abanin","full_name":"Abanin, Dmitry","first_name":"Dmitry"}],"acknowledgement":"We   acknowledge   useful   discussions with V. Kravtsov, T. Grover, and R. Vasseur.  M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307.  M.S. and D.A.  acknowledge  hospitality  of  KITP,  where  parts  of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","date_updated":"2023-09-26T15:51:54Z","article_number":"104201","abstract":[{"text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition.","lang":"eng"}],"date_published":"2017-09-06T00:00:00Z","_id":"834","title":"Thouless energy and multifractality across the many-body localization transition","publication_status":"published","citation":{"mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>.","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>.","short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10. American Physical Society, 2017.","apa":"Serbyn, M., Zlatko, P., &#38; Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201."},"date_created":"2018-12-11T11:48:45Z","publisher":"American Physical Society","department":[{"_id":"MaSe"}]},{"publication":"Special Sessions in Applications of Computer Algebra","isi":1,"doi":"10.1007/978-3-319-56932-1_8","project":[{"grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"volume":198,"quality_controlled":"1","external_id":{"isi":["000434088200008"]},"oa_version":"None","scopus_import":"1","day":"27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6812","alternative_title":["PROMS"],"month":"07","article_processing_charge":"No","year":"2017","language":[{"iso":"eng"}],"status":"public","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","citation":{"apa":"Ethier, M., Jablonski, G., &#38; Mrozek, M. (2017). Finding eigenvalues of self-maps with the Kronecker canonical form. In <i>Special Sessions in Applications of Computer Algebra</i> (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>","ama":"Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the Kronecker canonical form. In: <i>Special Sessions in Applications of Computer Algebra</i>. Vol 198. Springer; 2017:119-136. doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>","ieee":"M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps with the Kronecker canonical form,” in <i>Special Sessions in Applications of Computer Algebra</i>, Kalamata, Greece, 2017, vol. 198, pp. 119–136.","short":"M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications of Computer Algebra, Springer, 2017, pp. 119–136.","chicago":"Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” In <i>Special Sessions in Applications of Computer Algebra</i>, 198:119–36. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>.","mla":"Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” <i>Special Sessions in Applications of Computer Algebra</i>, vol. 198, Springer, 2017, pp. 119–36, doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>.","ista":"Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with the Kronecker canonical form. Special Sessions in Applications of Computer Algebra. ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136."},"date_created":"2018-12-11T11:48:46Z","ec_funded":1,"title":"Finding eigenvalues of self-maps with the Kronecker canonical form","_id":"836","date_published":"2017-07-27T00:00:00Z","conference":{"location":"Kalamata, Greece","name":"ACA: Applications of Computer Algebra","end_date":"2015-07-23","start_date":"2015-07-20"},"page":"119 - 136","abstract":[{"lang":"eng","text":"Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces."}],"date_updated":"2023-09-26T15:50:52Z","author":[{"full_name":"Ethier, Marc","first_name":"Marc","last_name":"Ethier"},{"orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski"},{"first_name":"Marian","full_name":"Mrozek, Marian","last_name":"Mrozek"}],"publication_identifier":{"isbn":["978-331956930-7"]},"intvolume":"       198","type":"conference"},{"supervisor":[{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"oa":1,"doi":"10.15479/AT:ISTA:th_858","alternative_title":["ISTA Thesis"],"publist_id":"6811","pubrep_id":"858","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"23","language":[{"iso":"eng"}],"year":"2017","status":"public","article_processing_charge":"No","month":"08","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"5828","status":"public"}]},"oa_version":"Published Version","date_created":"2018-12-11T11:48:46Z","citation":{"ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","apa":"Xu, H. (2017). <i>Reactivation of the hippocampal cognitive map in goal-directed spatial tasks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>.","mla":"Xu, Haibing. <i>Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017."},"publication_status":"published","date_published":"2017-08-23T00:00:00Z","_id":"837","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","file":[{"file_name":"2017_Xu_Haibing_Thesis_Source.docx","date_created":"2019-04-05T08:59:51Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"f11925fbbce31e495124b6bc4f10573c","date_updated":"2020-07-14T12:48:12Z","relation":"source_file","access_level":"closed","creator":"dernst","file_id":"6213","file_size":3589490},{"content_type":"application/pdf","file_name":"2017_Xu_Thesis_IST.pdf","date_created":"2019-04-05T08:59:51Z","creator":"dernst","file_id":"6214","file_size":11668613,"date_updated":"2020-07-14T12:48:12Z","checksum":"ffb10749a537d615fab1ef0937ccb157","relation":"main_file","access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"ddc":["571"],"type":"dissertation","date_updated":"2023-09-07T12:06:38Z","page":"93","abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:12Z","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","full_name":"Xu, Haibing","first_name":"Haibing"}]},{"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"ddc":["000"],"file_date_updated":"2020-07-14T12:48:12Z","author":[{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","first_name":"Michal","full_name":"Rybar, Michal"}],"date_updated":"2023-09-07T12:02:28Z","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k &gt; 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"page":"86","_id":"838","date_published":"2017-06-26T00:00:00Z","title":"(The exact security of) Message authentication codes","date_created":"2018-12-11T11:48:46Z","publication_status":"published","citation":{"short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","mla":"Rybar, Michal. <i>(The Exact Security of) Message Authentication Codes</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>.","chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>.","apa":"Rybar, M. (2017). <i>(The exact security of) Message authentication codes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria."},"degree_awarded":"PhD","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/pdf","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","date_created":"2018-12-12T10:10:13Z","creator":"system","file_size":847400,"file_id":"4799","checksum":"ff8639ec4bded6186f44c7bd3ee26804","date_updated":"2020-07-14T12:48:12Z","relation":"main_file","access_level":"open_access"},{"content_type":"application/zip","date_created":"2019-04-05T08:24:11Z","file_name":"2017_Thesis_Rybar_source.zip","creator":"dernst","file_id":"6202","file_size":26054879,"relation":"source_file","access_level":"closed","checksum":"3462101745ce8ad199c2d0f75dae4a7e","date_updated":"2020-07-14T12:48:12Z"}],"status":"public","year":"2017","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"06","pubrep_id":"828","alternative_title":["ISTA Thesis"],"publist_id":"6810","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"26","related_material":{"record":[{"status":"public","id":"2082","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6196"}]},"oa_version":"Published Version","has_accepted_license":"1","oa":1,"doi":"10.15479/AT:ISTA:th_828"}]