[{"status":"public","author":[{"first_name":"Andrey","full_name":"Grinshpun, Andrey","last_name":"Grinshpun"},{"last_name":"Phalitnonkiat","full_name":"Phalitnonkiat, Pakawat","first_name":"Pakawat"},{"full_name":"Rubin, Sasha","last_name":"Rubin","first_name":"Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tarfulea, Andrei","last_name":"Tarfulea","first_name":"Andrei"}],"doi":"10.1016/j.tcs.2013.11.032","date_published":"2014-02-13T00:00:00Z","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1303.3777","open_access":"1"}],"intvolume":"       521","abstract":[{"lang":"eng","text":"Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. "}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"13","publication":"Theoretical Computer Science","date_updated":"2021-01-12T06:56:16Z","volume":521,"department":[{"_id":"KrCh"}],"title":"Alternating traps in Muller and parity games","publist_id":"4703","page":"73 - 91","year":"2014","month":"02","publication_identifier":{"issn":["03043975"]},"quality_controlled":"1","publication_status":"published","_id":"2246","oa_version":"Submitted Version","type":"journal_article","citation":{"ama":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. 2014;521:73-91. doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>","short":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer Science 521 (2014) 73–91.","ista":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps in Muller and parity games. Theoretical Computer Science. 521, 73–91.","ieee":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps in Muller and parity games,” <i>Theoretical Computer Science</i>, vol. 521. Elsevier, pp. 73–91, 2014.","apa":"Grinshpun, A., Phalitnonkiat, P., Rubin, S., &#38; Tarfulea, A. (2014). Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>","chicago":"Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>.","mla":"Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>, vol. 521, Elsevier, 2014, pp. 73–91, doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>."},"date_created":"2018-12-11T11:56:33Z","oa":1,"publisher":"Elsevier"},{"scopus_import":1,"date_published":"2014-01-01T00:00:00Z","intvolume":"       322","abstract":[{"text":"Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","day":"01","volume":322,"date_updated":"2021-01-12T06:56:16Z","status":"public","author":[{"id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Capek, Daniel","last_name":"Capek","orcid":"0000-0001-5199-9940"},{"first_name":"Brian","full_name":"Metscher, Brian","last_name":"Metscher"},{"full_name":"Müller, Gerd","last_name":"Müller","first_name":"Gerd"}],"doi":"10.1002/jez.b.22545","publication_status":"published","quality_controlled":"1","issue":"1","_id":"2248","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:56:33Z","citation":{"short":"D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 322 (2014) 1–12.","ieee":"D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic approach to avian digit homology,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 322, no. 1. Wiley-Blackwell, pp. 1–12, 2014.","ista":"Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 322(1), 1–12.","ama":"Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach to avian digit homology. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2014;322(1):1-12. doi:<a href=\"https://doi.org/10.1002/jez.b.22545\">10.1002/jez.b.22545</a>","mla":"Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12, doi:<a href=\"https://doi.org/10.1002/jez.b.22545\">10.1002/jez.b.22545</a>.","chicago":"Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic Approach to Avian Digit Homology.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/jez.b.22545\">https://doi.org/10.1002/jez.b.22545</a>.","apa":"Capek, D., Metscher, B., &#38; Müller, G. (2014). Thumbs down: A molecular-morphogenetic approach to avian digit homology. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/jez.b.22545\">https://doi.org/10.1002/jez.b.22545</a>"},"publisher":"Wiley-Blackwell","department":[{"_id":"CaHe"}],"title":"Thumbs down: A molecular-morphogenetic approach to avian digit homology","publist_id":"4701","page":"1 - 12","year":"2014","month":"01","publication_identifier":{"issn":["15525007"]}},{"doi":"10.1111/tpj.12373","date_published":"2014-01-01T00:00:00Z","intvolume":"        77","publication":"Plant Journal","day":"01","volume":77,"title":"Inter-regulation of the unfolded protein response and auxin signaling","page":"97 - 107","publist_id":"4699","quality_controlled":"1","date_created":"2018-12-11T11:56:34Z","citation":{"ieee":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation of the unfolded protein response and auxin signaling,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.","short":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal 77 (2014) 97–107.","ista":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107.","ama":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. 2014;77(1):97-107. doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>","mla":"Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107, doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>.","chicago":"Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>.","apa":"Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., &#38; Brandizzí, F. (2014). Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>"},"oa":1,"status":"public","author":[{"last_name":"Chen","full_name":"Chen, Yani","first_name":"Yani"},{"first_name":"Kyaw","last_name":"Aung","full_name":"Aung, Kyaw"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"first_name":"Kathryn","full_name":"Walicki, Kathryn","last_name":"Walicki"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí"},{"last_name":"Brandizzí","full_name":"Brandizzí, Federica","first_name":"Federica"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/"}],"abstract":[{"text":"The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:56:17Z","department":[{"_id":"JiFr"}],"month":"01","year":"2014","publication_identifier":{"issn":["09607412"]},"publication_status":"published","issue":"1","_id":"2249","oa_version":"Submitted Version","type":"journal_article","publisher":"Wiley-Blackwell"},{"file_date_updated":"2020-07-14T12:45:34Z","doi":"10.1098/rstb.2012.0528","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"volume":369,"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","acknowledgement":"CC BY 3.0","day":"05","date_published":"2014-02-05T00:00:00Z","has_accepted_license":"1","intvolume":"       369","publist_id":"4697","title":"Sharp wave/ripple network oscillations and learning-associated hippocampal maps","article_number":"20120528","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:56:34Z","citation":{"apa":"Csicsvari, J. L., &#38; Dupret, D. (2014). Sharp wave/ripple network oscillations and learning-associated hippocampal maps. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2012.0528\">https://doi.org/10.1098/rstb.2012.0528</a>","chicago":"Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2014. <a href=\"https://doi.org/10.1098/rstb.2012.0528\">https://doi.org/10.1098/rstb.2012.0528</a>.","mla":"Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations and Learning-Associated Hippocampal Maps.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 369, no. 1635, 20120528, Royal Society, The, 2014, doi:<a href=\"https://doi.org/10.1098/rstb.2012.0528\">10.1098/rstb.2012.0528</a>.","ama":"Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2014;369(1635). doi:<a href=\"https://doi.org/10.1098/rstb.2012.0528\">10.1098/rstb.2012.0528</a>","short":"J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 369 (2014).","ista":"Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated hippocampal maps. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 369(1635), 20120528.","ieee":"J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and learning-associated hippocampal maps,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 369, no. 1635. Royal Society, The, 2014."},"author":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dupret","full_name":"Dupret, David","first_name":"David"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:18Z","scopus_import":1,"abstract":[{"text":"Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps.","lang":"eng"}],"month":"02","year":"2014","publication_identifier":{"issn":["09628436"]},"department":[{"_id":"JoCs"}],"pubrep_id":"527","publisher":"Royal Society, The","_id":"2251","issue":"1635","publication_status":"published","external_id":{"pmid":["24366138"]},"type":"journal_article","file":[{"date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:13:24Z","checksum":"51beb33de71c9c19e0c205a20d206f9a","file_size":771896,"file_name":"IST-2016-527-v1+1_20120528.full.pdf","relation":"main_file","creator":"system","file_id":"5006"}],"ddc":["570"],"oa_version":"Published Version"},{"scopus_import":"1","date_published":"2014-01-01T00:00:00Z","intvolume":"       105","abstract":[{"lang":"eng","text":"The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"01","publication":"Journal of Heredity","date_updated":"2022-08-25T14:45:42Z","volume":105,"status":"public","article_processing_charge":"No","author":[{"first_name":"Sujal","last_name":"Phadke","full_name":"Phadke, Sujal"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Pham","full_name":"Pham, Tuan","first_name":"Tuan"},{"first_name":"Stephanie","last_name":"Pham","full_name":"Pham, Stephanie"},{"first_name":"Rebecca","full_name":"Zufall, Rebecca","last_name":"Zufall"}],"doi":"10.1093/jhered/est063","quality_controlled":"1","publication_status":"published","issue":"1","_id":"2252","oa_version":"None","type":"journal_article","date_created":"2018-12-11T11:56:35Z","citation":{"short":"S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105 (2014) 130–135.","ista":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal of Heredity. 105(1), 130–135.","ieee":"S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila,” <i>Journal of Heredity</i>, vol. 105, no. 1. Oxford University Press, pp. 130–135, 2014.","ama":"Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. 2014;105(1):130-135. doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>","mla":"Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>, vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:<a href=\"https://doi.org/10.1093/jhered/est063\">10.1093/jhered/est063</a>.","chicago":"Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall. “Genetic Background Alters Dominance Relationships between Mat Alleles in the Ciliate Tetrahymena Thermophila.” <i>Journal of Heredity</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>.","apa":"Phadke, S., Paixao, T., Pham, T., Pham, S., &#38; Zufall, R. (2014). Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila. <i>Journal of Heredity</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jhered/est063\">https://doi.org/10.1093/jhered/est063</a>"},"publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"title":"Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila","publist_id":"4695","page":"130 - 135","year":"2014","month":"01","publication_identifier":{"issn":["00221503"]}},{"title":"Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth","publist_id":"4694","page":"108 - 118","citation":{"chicago":"Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>.","apa":"Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., … Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>","mla":"Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>.","ieee":"A. Bailly <i>et al.</i>, “Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.","short":"A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz, J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.","ista":"Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 77(1), 108–118.","ama":"Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. 2014;77(1):108-118. doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>"},"date_created":"2018-12-11T11:56:35Z","quality_controlled":"1","oa":1,"article_processing_charge":"No","doi":"10.1111/tpj.12369","intvolume":"        77","date_published":"2014-01-01T00:00:00Z","day":"01","publication":"Plant Journal","volume":77,"department":[{"_id":"JiFr"}],"article_type":"original","publication_identifier":{"issn":["09607412"]},"project":[{"name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur","_id":"256BDAB0-B435-11E9-9278-68D0E5697425"}],"year":"2014","month":"01","type":"journal_article","oa_version":"Published Version","publication_status":"published","issue":"1","_id":"2253","publisher":"Wiley-Blackwell","status":"public","author":[{"first_name":"Aurélien","last_name":"Bailly","full_name":"Bailly, Aurélien"},{"full_name":"Wang, Bangjun","last_name":"Wang","first_name":"Bangjun"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"last_name":"Pollmann","full_name":"Pollmann, Stephan","first_name":"Stephan"},{"first_name":"Daniel","last_name":"Schenck","full_name":"Schenck, Daniel"},{"last_name":"Lüthen","full_name":"Lüthen, Hartwig","first_name":"Hartwig"},{"last_name":"Schulz","full_name":"Schulz, Alexander","first_name":"Alexander"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"}],"main_file_link":[{"url":"https://doi.org/10.1111/tpj.12369","open_access":"1"}],"abstract":[{"text":"Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T06:56:18Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pubrep_id":"422","publisher":"Elsevier","_id":"2254","issue":"1","publication_status":"published","type":"journal_article","ddc":["570"],"file":[{"file_id":"4773","creator":"system","relation":"main_file","file_name":"IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf","file_size":4373072,"checksum":"438547cfcd9045a22f065f2019f07849","date_created":"2018-12-12T10:09:48Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:35Z"}],"oa_version":"Published Version","year":"2014","month":"01","project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"},{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF"}],"publication_identifier":{"issn":["08966273"]},"department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:56:19Z","scopus_import":1,"abstract":[{"text":"Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus.","lang":"eng"}],"author":[{"full_name":"Pernia-Andrade, Alejandro","last_name":"Pernia-Andrade","first_name":"Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"status":"public","oa":1,"quality_controlled":"1","citation":{"apa":"Pernia-Andrade, A., &#38; Jonas, P. M. (2014). Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>","chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>.","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>.","ama":"Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. 2014;81(1):140-152. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>","ieee":"A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations,” <i>Neuron</i>, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.","ista":"Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 81(1), 140–152.","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152."},"date_created":"2018-12-11T11:56:35Z","publist_id":"4692","page":"140 - 152","title":"Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations","volume":81,"publication":"Neuron","day":"08","date_published":"2014-01-08T00:00:00Z","intvolume":"        81","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:35Z","doi":"10.1016/j.neuron.2013.09.046","ec_funded":1},{"ec_funded":1,"file_date_updated":"2020-07-14T12:45:35Z","doi":"10.1007/s10851-013-0468-x","date_published":"2014-09-01T00:00:00Z","has_accepted_license":"1","intvolume":"        50","volume":50,"publication":"Journal of Mathematical Imaging and Vision","day":"01","title":"Stable length estimates of tube-like shapes","publist_id":"4691","page":"164 - 177","quality_controlled":"1","date_created":"2018-12-11T11:56:36Z","citation":{"ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. <i>Journal of Mathematical Imaging and Vision</i>. 2014;50(1):164-177. doi:<a href=\"https://doi.org/10.1007/s10851-013-0468-x\">10.1007/s10851-013-0468-x</a>","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, no. 1. Springer, pp. 164–177, 2014.","short":"H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision 50 (2014) 164–177.","ista":"Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 50(1), 164–177.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, no. 1, Springer, 2014, pp. 164–77, doi:<a href=\"https://doi.org/10.1007/s10851-013-0468-x\">10.1007/s10851-013-0468-x</a>.","apa":"Edelsbrunner, H., &#38; Pausinger, F. (2014). Stable length estimates of tube-like shapes. <i>Journal of Mathematical Imaging and Vision</i>. Springer. <a href=\"https://doi.org/10.1007/s10851-013-0468-x\">https://doi.org/10.1007/s10851-013-0468-x</a>","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” <i>Journal of Mathematical Imaging and Vision</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s10851-013-0468-x\">https://doi.org/10.1007/s10851-013-0468-x</a>."},"oa":1,"author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768"}],"status":"public","scopus_import":1,"abstract":[{"text":"Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm.","lang":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2843"},{"relation":"dissertation_contains","status":"public","id":"1399"}]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T11:41:25Z","department":[{"_id":"HeEd"}],"year":"2014","month":"09","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493"}],"publication_identifier":{"issn":["09249907"]},"_id":"2255","issue":"1","publication_status":"published","type":"journal_article","ddc":["000"],"oa_version":"Submitted Version","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:35Z","checksum":"2f93f3e63a38a85cd4404d7953913b14","file_size":3941391,"date_created":"2018-12-12T10:16:18Z","file_name":"IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf","creator":"system","file_id":"5204","relation":"main_file"}],"pubrep_id":"549","publisher":"Springer"},{"article_number":"e1003408","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:56:36Z","citation":{"ama":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. <i>PLoS Computational Biology</i>. 2014;10(1). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">10.1371/journal.pcbi.1003408</a>","short":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).","ista":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 10(1), e1003408.","ieee":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” <i>PLoS Computational Biology</i>, vol. 10, no. 1. Public Library of Science, 2014.","mla":"Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” <i>PLoS Computational Biology</i>, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">10.1371/journal.pcbi.1003408</a>.","apa":"Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., &#38; Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">https://doi.org/10.1371/journal.pcbi.1003408</a>","chicago":"Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” <i>PLoS Computational Biology</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003408\">https://doi.org/10.1371/journal.pcbi.1003408</a>."},"publist_id":"4689","title":"Searching for collective behavior in a large network of sensory neurons","volume":10,"publication":"PLoS Computational Biology","day":"02","acknowledgement":"\r\n\r\n\r\n\r\nThis work was funded by NSF grant IIS-0613435, NSF grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508, the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation, ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES: ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651.","date_published":"2014-01-02T00:00:00Z","has_accepted_license":"1","intvolume":"        10","file_date_updated":"2020-07-14T12:45:35Z","doi":"10.1371/journal.pcbi.1003408","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"436","publisher":"Public Library of Science","_id":"2257","issue":"1","publication_status":"published","oa_version":"Published Version","ddc":["570"],"type":"journal_article","file":[{"checksum":"c720222c5e924a4acb17f23b9381a6ca","file_size":2194790,"date_created":"2018-12-12T10:12:46Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:35Z","creator":"system","file_id":"4965","relation":"main_file","file_name":"IST-2016-436-v1+1_journal.pcbi.1003408.pdf"}],"year":"2014","month":"01","publication_identifier":{"issn":["1553734X"]},"department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:46:14Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction."}],"main_file_link":[{"open_access":"1","url":"http://repository.ist.ac.at/id/eprint/436"}],"related_material":{"record":[{"id":"5562","relation":"popular_science","status":"public"}]},"author":[{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"first_name":"Dario","last_name":"Amodei","full_name":"Amodei, Dario"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"},{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"status":"public"},{"citation":{"mla":"Zhu, Fangfang, et al. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” <i>Nucleic Acids Research</i>, vol. 42, no. 5, e34, Oxford University Press, 2014, doi:<a href=\"https://doi.org/10.1093/nar/gkt1290\">10.1093/nar/gkt1290</a>.","chicago":"Zhu, Fangfang, Matthew Gamboa, Alfonso Farruggio, Simon Hippenmeyer, Bosiljka Tasic, Birgitt Schüle, Yanru Chen Tsai, and Michele Calos. “DICE, an Efficient System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” <i>Nucleic Acids Research</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/nar/gkt1290\">https://doi.org/10.1093/nar/gkt1290</a>.","apa":"Zhu, F., Gamboa, M., Farruggio, A., Hippenmeyer, S., Tasic, B., Schüle, B., … Calos, M. (2014). DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkt1290\">https://doi.org/10.1093/nar/gkt1290</a>","ieee":"F. Zhu <i>et al.</i>, “DICE, an efficient system for iterative genomic editing in human pluripotent stem cells,” <i>Nucleic Acids Research</i>, vol. 42, no. 5. Oxford University Press, 2014.","short":"F. Zhu, M. Gamboa, A. Farruggio, S. Hippenmeyer, B. Tasic, B. Schüle, Y. Chen Tsai, M. Calos, Nucleic Acids Research 42 (2014).","ista":"Zhu F, Gamboa M, Farruggio A, Hippenmeyer S, Tasic B, Schüle B, Chen Tsai Y, Calos M. 2014. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. Nucleic Acids Research. 42(5), e34.","ama":"Zhu F, Gamboa M, Farruggio A, et al. DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. <i>Nucleic Acids Research</i>. 2014;42(5). doi:<a href=\"https://doi.org/10.1093/nar/gkt1290\">10.1093/nar/gkt1290</a>"},"date_created":"2018-12-11T11:56:38Z","quality_controlled":"1","oa":1,"article_number":"e34","title":"DICE, an efficient system for iterative genomic editing in human pluripotent stem cells","publist_id":"4684","has_accepted_license":"1","intvolume":"        42","date_published":"2014-03-05T00:00:00Z","day":"05","acknowledgement":"California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]. Funding for open access charge: California Institute for Regenerative Medicine [RT2-01880 and TR2-01756]\r\nCC BY 3,0","publication":"Nucleic Acids Research","volume":42,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1093/nar/gkt1290","file_date_updated":"2020-07-14T12:45:35Z","oa_version":"Preprint","file":[{"date_updated":"2020-07-14T12:45:35Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:09:15Z","file_size":11044478,"checksum":"e9268f5f96a820f04d7ebbf85927c3cb","file_name":"IST-2018-961-v1+1_2014_Hippenmeyer_DICE.pdf","relation":"main_file","file_id":"4738","creator":"system"}],"type":"journal_article","ddc":["571","610"],"publication_status":"published","issue":"5","_id":"2261","publisher":"Oxford University Press","pubrep_id":"961","department":[{"_id":"SiHi"}],"month":"03","year":"2014","abstract":[{"lang":"eng","text":"To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus."}],"scopus_import":1,"date_updated":"2021-01-12T06:56:22Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"first_name":"Fangfang","last_name":"Zhu","full_name":"Zhu, Fangfang"},{"first_name":"Matthew","last_name":"Gamboa","full_name":"Gamboa, Matthew"},{"first_name":"Alfonso","full_name":"Farruggio, Alfonso","last_name":"Farruggio"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tasic","full_name":"Tasic, Bosiljka","first_name":"Bosiljka"},{"last_name":"Schüle","full_name":"Schüle, Birgitt","first_name":"Birgitt"},{"first_name":"Yanru","last_name":"Chen Tsai","full_name":"Chen Tsai, Yanru"},{"first_name":"Michele","last_name":"Calos","full_name":"Calos, Michele"}]},{"editor":[{"first_name":"Laurent","full_name":"Nguyen, Laurent","last_name":"Nguyen"}],"intvolume":"       800","abstract":[{"lang":"eng","text":"Coordinated migration of newly-born neurons to their target territories is essential for correct neuronal circuit assembly in the developing brain. Although a cohort of signaling pathways has been implicated in the regulation of cortical projection neuron migration, the precise molecular mechanisms and how a balanced interplay of cell-autonomous and non-autonomous functions of candidate signaling molecules controls the discrete steps in the migration process, are just being revealed. In this chapter, I will focally review recent advances that improved our understanding of the cell-autonomous and possible cell-nonautonomous functions of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential steps of cortical projection neuron migration. I will then elaborate on the emerging concept that the Reelin signaling pathway, acts exactly at precise stages in the course of cortical projection neuron migration. Lastly, I will discuss how finely tuned transcriptional programs and downstream effectors govern particular aspects in driving radial migration at discrete stages and how they regulate the precise positioning of cortical projection neurons in the developing cerebral cortex."}],"date_published":"2014-01-01T00:00:00Z","scopus_import":1,"day":"01","publication":" Cellular and Molecular Control of Neuronal Migration","date_updated":"2021-01-12T06:56:23Z","volume":800,"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"doi":"10.1007/978-94-007-7687-6_1","oa_version":"None","type":"book_chapter","date_created":"2018-12-11T11:56:39Z","citation":{"ama":"Hippenmeyer S. Molecular pathways controlling the sequential steps of cortical projection neuron migration. In: Nguyen L, ed. <i> Cellular and Molecular Control of Neuronal Migration</i>. Vol 800. Springer; 2014:1-24. doi:<a href=\"https://doi.org/10.1007/978-94-007-7687-6_1\">10.1007/978-94-007-7687-6_1</a>","ieee":"S. Hippenmeyer, “Molecular pathways controlling the sequential steps of cortical projection neuron migration,” in <i> Cellular and Molecular Control of Neuronal Migration</i>, vol. 800, L. Nguyen, Ed. Springer, 2014, pp. 1–24.","short":"S. Hippenmeyer, in:, L. Nguyen (Ed.),  Cellular and Molecular Control of Neuronal Migration, Springer, 2014, pp. 1–24.","ista":"Hippenmeyer S. 2014.Molecular pathways controlling the sequential steps of cortical projection neuron migration. In:  Cellular and Molecular Control of Neuronal Migration. Advances in Experimental Medicine and Biology, vol. 800, 1–24.","apa":"Hippenmeyer, S. (2014). Molecular pathways controlling the sequential steps of cortical projection neuron migration. In L. Nguyen (Ed.), <i> Cellular and Molecular Control of Neuronal Migration</i> (Vol. 800, pp. 1–24). Springer. <a href=\"https://doi.org/10.1007/978-94-007-7687-6_1\">https://doi.org/10.1007/978-94-007-7687-6_1</a>","chicago":"Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps of Cortical Projection Neuron Migration.” In <i> Cellular and Molecular Control of Neuronal Migration</i>, edited by Laurent Nguyen, 800:1–24. Springer, 2014. <a href=\"https://doi.org/10.1007/978-94-007-7687-6_1\">https://doi.org/10.1007/978-94-007-7687-6_1</a>.","mla":"Hippenmeyer, Simon. “Molecular Pathways Controlling the Sequential Steps of Cortical Projection Neuron Migration.” <i> Cellular and Molecular Control of Neuronal Migration</i>, edited by Laurent Nguyen, vol. 800, Springer, 2014, pp. 1–24, doi:<a href=\"https://doi.org/10.1007/978-94-007-7687-6_1\">10.1007/978-94-007-7687-6_1</a>."},"publication_status":"published","alternative_title":["Advances in Experimental Medicine and Biology"],"quality_controlled":"1","_id":"2265","publisher":"Springer","department":[{"_id":"SiHi"}],"title":"Molecular pathways controlling the sequential steps of cortical projection neuron migration","publist_id":"4679","page":"1 - 24","year":"2014","month":"01"},{"quality_controlled":"1","conference":{"name":"ICCV: International Conference on Computer Vision","start_date":"2013-12-01","location":"Sydney, Australia","end_date":"2013-12-08"},"citation":{"chicago":"Olsson, Carl, Johannes Ulen, Yuri Boykov, and Vladimir Kolmogorov. “Partial Enumeration and Curvature Regularization,” 2936–43. IEEE, 2014. <a href=\"https://doi.org/10.1109/ICCV.2013.365\">https://doi.org/10.1109/ICCV.2013.365</a>.","apa":"Olsson, C., Ulen, J., Boykov, Y., &#38; Kolmogorov, V. (2014). Partial enumeration and curvature regularization (pp. 2936–2943). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2013.365\">https://doi.org/10.1109/ICCV.2013.365</a>","mla":"Olsson, Carl, et al. <i>Partial Enumeration and Curvature Regularization</i>. IEEE, 2014, pp. 2936–43, doi:<a href=\"https://doi.org/10.1109/ICCV.2013.365\">10.1109/ICCV.2013.365</a>.","ieee":"C. Olsson, J. Ulen, Y. Boykov, and V. Kolmogorov, “Partial enumeration and curvature regularization,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2014, pp. 2936–2943.","short":"C. Olsson, J. Ulen, Y. Boykov, V. Kolmogorov, in:, IEEE, 2014, pp. 2936–2943.","ista":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. 2014. Partial enumeration and curvature regularization. ICCV: International Conference on Computer Vision, 2936–2943.","ama":"Olsson C, Ulen J, Boykov Y, Kolmogorov V. Partial enumeration and curvature regularization. In: IEEE; 2014:2936-2943. doi:<a href=\"https://doi.org/10.1109/ICCV.2013.365\">10.1109/ICCV.2013.365</a>"},"date_created":"2018-12-11T11:56:42Z","oa":1,"title":"Partial enumeration and curvature regularization","page":"2936 - 2943","publist_id":"4669","date_published":"2014-03-03T00:00:00Z","has_accepted_license":"1","day":"03","file_date_updated":"2020-07-14T12:45:36Z","doi":"10.1109/ICCV.2013.365","publication_status":"published","_id":"2275","oa_version":"Submitted Version","type":"conference","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:36Z","file_size":378601,"checksum":"4a74b5c92d6dcd2348c2c10ec8dd18bf","date_created":"2018-12-12T10:09:30Z","file_name":"IST-2016-566-v1+1_iccv13_part_enumeration.pdf","file_id":"4754","creator":"system","relation":"main_file"}],"ddc":["000"],"publisher":"IEEE","pubrep_id":"566","department":[{"_id":"VlKo"}],"month":"03","year":"2014","scopus_import":1,"abstract":[{"text":"Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches. \r\nThis partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed. \r\nOur main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach.\r\n","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:28Z","status":"public","author":[{"first_name":"Carl","full_name":"Olsson, Carl","last_name":"Olsson"},{"first_name":"Johannes","last_name":"Ulen","full_name":"Ulen, Johannes"},{"full_name":"Boykov, Yuri","last_name":"Boykov","first_name":"Yuri"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}]},{"author":[{"last_name":"Guo","full_name":"Guo, Yujin","first_name":"Yujin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"status":"public","date_updated":"2024-02-14T12:19:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential.","lang":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1301.5682","open_access":"1"}],"scopus_import":"1","month":"02","year":"2014","department":[{"_id":"RoSe"}],"article_type":"original","publisher":"Springer","type":"journal_article","oa_version":"Preprint","_id":"2281","issue":"2","external_id":{"arxiv":["1301.5682"]},"publication_status":"published","doi":"10.1007/s11005-013-0667-9","article_processing_charge":"No","volume":104,"publication":"Letters in Mathematical Physics","day":"01","intvolume":"       104","date_published":"2014-02-01T00:00:00Z","page":"141 - 156","publist_id":"4653","title":"On the mass concentration for Bose-Einstein condensates with attractive interactions","oa":1,"citation":{"chicago":"Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein Condensates with Attractive Interactions.” <i>Letters in Mathematical Physics</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s11005-013-0667-9\">https://doi.org/10.1007/s11005-013-0667-9</a>.","apa":"Guo, Y., &#38; Seiringer, R. (2014). On the mass concentration for Bose-Einstein condensates with attractive interactions. <i>Letters in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s11005-013-0667-9\">https://doi.org/10.1007/s11005-013-0667-9</a>","mla":"Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein Condensates with Attractive Interactions.” <i>Letters in Mathematical Physics</i>, vol. 104, no. 2, Springer, 2014, pp. 141–56, doi:<a href=\"https://doi.org/10.1007/s11005-013-0667-9\">10.1007/s11005-013-0667-9</a>.","short":"Y. Guo, R. Seiringer, Letters in Mathematical Physics 104 (2014) 141–156.","ieee":"Y. Guo and R. Seiringer, “On the mass concentration for Bose-Einstein condensates with attractive interactions,” <i>Letters in Mathematical Physics</i>, vol. 104, no. 2. Springer, pp. 141–156, 2014.","ista":"Guo Y, Seiringer R. 2014. On the mass concentration for Bose-Einstein condensates with attractive interactions. Letters in Mathematical Physics. 104(2), 141–156.","ama":"Guo Y, Seiringer R. On the mass concentration for Bose-Einstein condensates with attractive interactions. <i>Letters in Mathematical Physics</i>. 2014;104(2):141-156. doi:<a href=\"https://doi.org/10.1007/s11005-013-0667-9\">10.1007/s11005-013-0667-9</a>"},"date_created":"2018-12-11T11:56:44Z","arxiv":1,"quality_controlled":"1"},{"publist_id":"4646","page":"189 - 203","title":"Morpho-physiological criteria divide dentate gyrus interneurons into classes","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:56:46Z","citation":{"ama":"Hosp J, Strüber M, Yanagawa Y, et al. Morpho-physiological criteria divide dentate gyrus interneurons into classes. <i>Hippocampus</i>. 2014;23(2):189-203. doi:<a href=\"https://doi.org/10.1002/hipo.22214\">10.1002/hipo.22214</a>","ieee":"J. Hosp <i>et al.</i>, “Morpho-physiological criteria divide dentate gyrus interneurons into classes,” <i>Hippocampus</i>, vol. 23, no. 2. Wiley-Blackwell, pp. 189–203, 2014.","ista":"Hosp J, Strüber M, Yanagawa Y, Obata K, Vida I, Jonas PM, Bartos M. 2014. Morpho-physiological criteria divide dentate gyrus interneurons into classes. Hippocampus. 23(2), 189–203.","short":"J. Hosp, M. Strüber, Y. Yanagawa, K. Obata, I. Vida, P.M. Jonas, M. Bartos, Hippocampus 23 (2014) 189–203.","mla":"Hosp, Jonas, et al. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons into Classes.” <i>Hippocampus</i>, vol. 23, no. 2, Wiley-Blackwell, 2014, pp. 189–203, doi:<a href=\"https://doi.org/10.1002/hipo.22214\">10.1002/hipo.22214</a>.","apa":"Hosp, J., Strüber, M., Yanagawa, Y., Obata, K., Vida, I., Jonas, P. M., &#38; Bartos, M. (2014). Morpho-physiological criteria divide dentate gyrus interneurons into classes. <i>Hippocampus</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/hipo.22214\">https://doi.org/10.1002/hipo.22214</a>","chicago":"Hosp, Jonas, Michael Strüber, Yuchio Yanagawa, Kunihiko Obata, Imre Vida, Peter M Jonas, and Marlene Bartos. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons into Classes.” <i>Hippocampus</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/hipo.22214\">https://doi.org/10.1002/hipo.22214</a>."},"file_date_updated":"2020-07-14T12:45:37Z","doi":"10.1002/hipo.22214","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"day":"01","publication":"Hippocampus","acknowledgement":"Funded by Deutsche Forschungsgemeinschaft. Grant Numbers: SFB 505, SFB 780, BA1582/2-1 Excellence Initiative of the German Research Foundation (Spemann Graduate School). Grant Number: GSC-4 Lichtenberg Professorship-Award (VW-Foundation); Schram-Foundation; Excellence Initiative Brain Links-Brain Tools. The authors thank Drs. Jonas-Frederic Sauer and Claudio Elgueta for critically reading the manuscript. They also thank Karin Winterhalter, Margit Northemann and Ulrich Nöller for technical assistance.","volume":23,"date_published":"2014-02-01T00:00:00Z","intvolume":"        23","has_accepted_license":"1","month":"02","year":"2014","department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","pubrep_id":"461","publication_status":"published","issue":"2","_id":"2285","file":[{"file_name":"IST-2016-461-v1+1_Hosp_et_al-2014-Hippocampus.pdf","relation":"main_file","creator":"system","file_id":"5178","date_updated":"2020-07-14T12:45:37Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:15:54Z","checksum":"ff6bc75a79dbc985a2e31b79253e6444","file_size":801589}],"ddc":["570"],"oa_version":"Published Version","type":"journal_article","license":"https://creativecommons.org/licenses/by-nc/4.0/","status":"public","author":[{"full_name":"Hosp, Jonas","last_name":"Hosp","first_name":"Jonas"},{"first_name":"Michael","full_name":"Strüber, Michael","last_name":"Strüber"},{"first_name":"Yuchio","last_name":"Yanagawa","full_name":"Yanagawa, Yuchio"},{"first_name":"Kunihiko","last_name":"Obata","full_name":"Obata, Kunihiko"},{"first_name":"Imre","last_name":"Vida","full_name":"Vida, Imre"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"},{"first_name":"Marlene","last_name":"Bartos","full_name":"Bartos, Marlene"}],"user_id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:56:32Z","scopus_import":1,"abstract":[{"text":"GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity.","lang":"eng"}]},{"doi":"10.1007/978-3-319-05957-0","status":"public","author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"article_processing_charge":"No","place":"Cham","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","date_updated":"2022-03-04T07:47:54Z","series_title":"SpringerBriefs in Applied Sciences and Technology","scopus_import":"1","date_published":"2014-01-01T00:00:00Z","related_material":{"link":[{"description":"available as eBook via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106","relation":"other"},{"url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842","relation":"other","description":"available via catalog IST BookList"}]},"abstract":[{"text":"This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.","lang":"eng"}],"page":"IX, 110","year":"2014","month":"01","publication_identifier":{"eissn":["2191-5318"],"eisbn":["9-783-3190-5957-0"],"isbn":["9-783-3190-5956-3"],"issn":["2191-530X"]},"edition":"1","department":[{"_id":"HeEd"}],"title":"A Short Course in Computational Geometry and Topology","publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"_id":"6853","oa_version":"None","type":"book","citation":{"chicago":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>.","apa":"Edelsbrunner, H. (2014). <i>A Short Course in Computational Geometry and Topology</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>","mla":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>.","ieee":"H. Edelsbrunner, <i>A Short Course in Computational Geometry and Topology</i>, 1st ed. Cham: Springer Nature, 2014.","ista":"Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p.","short":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014.","ama":"Edelsbrunner H. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. Cham: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>"},"date_created":"2019-09-06T09:22:33Z"},{"department":[{"_id":"VlKo"},{"_id":"UlWa"}],"title":"Playful Math - An introduction to mathematical games","page":"5","year":"2014","month":"06","publication_status":"draft","_id":"7038","oa_version":"Published Version","ddc":["510"],"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:48Z","checksum":"2b94e5e1f4c3fe8ab89b12806276fb09","file_size":511233,"date_created":"2019-11-18T15:57:51Z","file_name":"2014_Playful_Math_Huszar.pdf","file_id":"7039","creator":"dernst","relation":"main_file"}],"type":"working_paper","citation":{"apa":"Huszár, K., &#38; Rolinek, M. (n.d.). <i>Playful Math - An introduction to mathematical games</i>. IST Austria.","chicago":"Huszár, Kristóf, and Michal Rolinek. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria, n.d.","mla":"Huszár, Kristóf, and Michal Rolinek. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria.","ama":"Huszár K, Rolinek M. <i>Playful Math - An Introduction to Mathematical Games</i>. IST Austria","ista":"Huszár K, Rolinek M. Playful Math - An introduction to mathematical games, IST Austria, 5p.","ieee":"K. Huszár and M. Rolinek, <i>Playful Math - An introduction to mathematical games</i>. IST Austria.","short":"K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games, IST Austria, n.d."},"date_created":"2019-11-18T15:57:05Z","oa":1,"publisher":"IST Austria","status":"public","author":[{"first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","last_name":"Huszár","full_name":"Huszár, Kristóf"},{"first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","last_name":"Rolinek"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:48Z","date_published":"2014-06-30T00:00:00Z","has_accepted_license":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","date_updated":"2020-07-14T23:11:45Z"},{"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:00:53Z","scopus_import":1,"abstract":[{"text":"First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard. ","lang":"eng"}],"status":"public","author":[{"first_name":"Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","full_name":"Aminof, Benjamin","last_name":"Aminof"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","last_name":"Rubin","full_name":"Rubin, Sasha"}],"publisher":"Open Publishing Association","pubrep_id":"952","alternative_title":["EPTCS"],"publication_status":"published","_id":"475","oa_version":"Published Version","ddc":["004"],"type":"conference","file":[{"file_name":"IST-2018-952-v1+1_2014_Rubin_First_cycle.pdf","relation":"main_file","creator":"system","file_id":"5260","date_updated":"2020-07-14T12:46:35Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:17:08Z","file_size":100115,"checksum":"4d7b4ab82980cca2b96ac7703992a8c8"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"month":"04","year":"2014","department":[{"_id":"KrCh"}],"day":"01","publication":"Electronic Proceedings in Theoretical Computer Science, EPTCS","volume":146,"date_published":"2014-04-01T00:00:00Z","has_accepted_license":"1","intvolume":"       146","file_date_updated":"2020-07-14T12:46:35Z","doi":"10.4204/EPTCS.146.11","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"oa":1,"quality_controlled":"1","conference":{"name":"SR: Strategic Reasoning","start_date":"2014-04-05","end_date":"2014-04-06","location":"Grenoble, France"},"citation":{"ieee":"B. Aminof and S. Rubin, “First cycle games,” in <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, Grenoble, France, 2014, vol. 146, pp. 83–90.","short":"B. Aminof, S. Rubin, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing Association, 2014, pp. 83–90.","ista":"Aminof B, Rubin S. 2014. First cycle games. Electronic Proceedings in Theoretical Computer Science, EPTCS. SR: Strategic Reasoning, EPTCS, vol. 146, 83–90.","ama":"Aminof B, Rubin S. First cycle games. In: <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>. Vol 146. Open Publishing Association; 2014:83-90. doi:<a href=\"https://doi.org/10.4204/EPTCS.146.11\">10.4204/EPTCS.146.11</a>","chicago":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, 146:83–90. Open Publishing Association, 2014. <a href=\"https://doi.org/10.4204/EPTCS.146.11\">https://doi.org/10.4204/EPTCS.146.11</a>.","apa":"Aminof, B., &#38; Rubin, S. (2014). First cycle games. In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i> (Vol. 146, pp. 83–90). Grenoble, France: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.146.11\">https://doi.org/10.4204/EPTCS.146.11</a>","mla":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, vol. 146, Open Publishing Association, 2014, pp. 83–90, doi:<a href=\"https://doi.org/10.4204/EPTCS.146.11\">10.4204/EPTCS.146.11</a>."},"date_created":"2018-12-11T11:46:41Z","publist_id":"7345","page":"83 - 90","title":"First cycle games"},{"ec_funded":1,"article_processing_charge":"No","doi":"10.1007/s00453-013-9843-7","intvolume":"        70","date_published":"2014-11-01T00:00:00Z","volume":70,"publication":"Algorithmica","day":"01","title":"Polynomial-time algorithms for energy games with special weight structures","page":"457 - 492","publist_id":"7282","date_created":"2018-12-11T11:47:01Z","citation":{"chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithmica</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00453-013-9843-7\">https://doi.org/10.1007/s00453-013-9843-7</a>.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-013-9843-7\">https://doi.org/10.1007/s00453-013-9843-7</a>","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithmica</i>, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:<a href=\"https://doi.org/10.1007/s00453-013-9843-7\">10.1007/s00453-013-9843-7</a>.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” <i>Algorithmica</i>, vol. 70, no. 3. Springer, pp. 457–492, 2014.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. <i>Algorithmica</i>. 2014;70(3):457-492. doi:<a href=\"https://doi.org/10.1007/s00453-013-9843-7\">10.1007/s00453-013-9843-7</a>"},"quality_controlled":"1","arxiv":1,"oa":1,"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"status":"public","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help."}],"main_file_link":[{"url":"https://arxiv.org/abs/1604.08234","open_access":"1"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10905"}]},"scopus_import":"1","date_updated":"2023-09-05T14:09:29Z","language":[{"iso":"eng"}],"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","department":[{"_id":"KrCh"}],"article_type":"original","year":"2014","month":"11","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","oa_version":"Preprint","_id":"535","issue":"3","external_id":{"arxiv":["1604.08234"]},"publication_status":"published","publisher":"Springer"},{"status":"public","author":[{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak","full_name":"Prizak, Roshan"},{"first_name":"Thomas","last_name":"Ezard","full_name":"Ezard, Thomas"},{"first_name":"Rebecca","full_name":"Hoyle, Rebecca","last_name":"Hoyle"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:30Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring."}],"month":"07","year":"2014","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Wiley-Blackwell","pubrep_id":"934","publication_status":"published","_id":"537","issue":"15","file":[{"date_created":"2018-12-12T10:11:31Z","file_size":621582,"checksum":"e32abf75a248e7a11811fd7f60858769","date_updated":"2020-07-14T12:46:38Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"system","file_id":"4886","file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf"}],"type":"journal_article","ddc":["530","571"],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:38Z","doi":"10.1002/ece3.1150","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"19","publication":"Ecology and Evolution","volume":4,"date_published":"2014-07-19T00:00:00Z","has_accepted_license":"1","intvolume":"         4","publist_id":"7280","page":"3139 - 3145","title":"Fitness consequences of maternal and grandmaternal effects","oa":1,"date_created":"2018-12-11T11:47:02Z","citation":{"ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. 2014;4(15):3139-3145. doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>","ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” <i>Ecology and Evolution</i>, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>.","apa":"Prizak, R., Ezard, T., &#38; Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>","chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>."}},{"publication_identifier":{"issn":["2664-1690"]},"page":"20","month":"01","year":"2014","department":[{"_id":"ToHe"}],"title":"Compositional specifications for IOCO testing","publisher":"IST Austria","pubrep_id":"152","oa":1,"oa_version":"Published Version","type":"technical_report","ddc":["000"],"file":[{"date_created":"2018-12-12T11:54:21Z","file_size":534732,"checksum":"0e03aba625cc334141a3148432aa5760","date_updated":"2020-07-14T12:46:46Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"system","file_id":"5543","file_name":"IST-2014-148-v2+1_main_tr.pdf"}],"date_created":"2018-12-12T11:39:11Z","citation":{"ista":"Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing, IST Austria, 20p.","ieee":"P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, <i>Compositional specifications for IOCO testing</i>. IST Austria, 2014.","short":"P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, Compositional Specifications for IOCO Testing, IST Austria, 2014.","ama":"Daca P, Henzinger TA, Krenn W, Nickovic D. <i>Compositional Specifications for IOCO Testing</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">10.15479/AT:IST-2014-148-v2-1</a>","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. <i>Compositional Specifications for IOCO Testing</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">https://doi.org/10.15479/AT:IST-2014-148-v2-1</a>.","apa":"Daca, P., Henzinger, T. A., Krenn, W., &#38; Nickovic, D. (2014). <i>Compositional specifications for IOCO testing</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">https://doi.org/10.15479/AT:IST-2014-148-v2-1</a>","mla":"Daca, Przemyslaw, et al. <i>Compositional Specifications for IOCO Testing</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-148-v2-1\">10.15479/AT:IST-2014-148-v2-1</a>."},"publication_status":"published","alternative_title":["IST Austria Technical Report"],"_id":"5411","doi":"10.15479/AT:IST-2014-148-v2-1","file_date_updated":"2020-07-14T12:46:46Z","status":"public","author":[{"first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw","last_name":"Daca"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Willibald","full_name":"Krenn, Willibald","last_name":"Krenn"},{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"day":"28","date_updated":"2023-02-23T10:31:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"2167","status":"public","relation":"later_version"}]},"has_accepted_license":"1","abstract":[{"text":"Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing.\r\nIn this paper, we study compositional properties of the IOCO-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the IOCO conformance relation, the resulting methodology can be applied to a broader class of systems.","lang":"eng"}],"date_published":"2014-01-28T00:00:00Z"}]