[{"volume":35,"month":"08","page":"2669 - 2684","status":"public","author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"orcid":"0000-0003-0876-3187","last_name":"Chait","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"issue":"11","publication":"Molecular Biology and Evolution","intvolume":"        35","publist_id":"8036","date_updated":"2023-10-17T11:51:06Z","date_published":"2018-08-28T00:00:00Z","abstract":[{"lang":"eng","text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses."}],"citation":{"chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>","apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684."},"article_processing_charge":"No","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","publication_identifier":{"issn":["0737-4038"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publication_status":"published","publisher":"Oxford University Press","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"type":"journal_article","external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"pmid":1,"day":"28","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:44:11Z","isi":1,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy163","_id":"19","scopus_import":"1","oa_version":"Submitted Version"},{"quality_controlled":"1","isi":1,"date_created":"2018-12-11T11:45:06Z","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","oa_version":"Submitted Version","_id":"190","doi":"10.1002/jez.b.22824","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}],"department":[{"_id":"BeVi"}],"publisher":"Wiley","year":"2018","publication_status":"published","oa":1,"pmid":1,"external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"day":"11","type":"journal_article","intvolume":"       330","date_updated":"2023-09-11T13:59:54Z","publist_id":"7730","date_published":"2018-07-11T00:00:00Z","abstract":[{"text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control.","lang":"eng"}],"citation":{"ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>.","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>"},"month":"07","volume":330,"page":"254-264","author":[{"last_name":"Harrison","first_name":"Mark","full_name":"Harrison, Mark"},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"full_name":"Kremer, Lucas","first_name":"Lucas","last_name":"Kremer"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"last_name":"Belles","first_name":"Xavier","full_name":"Belles, Xavier"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"},{"first_name":"Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jongepier, Evelien","first_name":"Evelien","last_name":"Jongepier"},{"first_name":"Maria","last_name":"Puilachs","full_name":"Puilachs, Maria"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"}],"status":"public","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution"},{"quality_controlled":"1","date_created":"2018-12-11T11:45:07Z","isi":1,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0190-1","_id":"192","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"type":"journal_article","day":"25","external_id":{"pmid":["29942048"],"isi":["000443221200017"]},"pmid":1,"oa":1,"intvolume":"         4","publist_id":"7728","date_updated":"2023-09-15T12:11:03Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/","relation":"press_release","description":"News on IST Homepage"}]},"date_published":"2018-06-25T00:00:00Z","abstract":[{"text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.","lang":"eng"}],"citation":{"apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>.","ieee":"M. Fendrych <i>et al.</i>, “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” <i>Nature Plants</i>, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. 2018;4(7):453-459. doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459."},"volume":4,"month":"06","page":"453 - 459","status":"public","author":[{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699"},{"first_name":"Maria","orcid":"0000-0003-1522-3162","last_name":"Akhmanova","full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"first_name":"Shinya","last_name":"Hagihara","full_name":"Hagihara, Shinya"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"full_name":"Uchida, Naoyuki","first_name":"Naoyuki","last_name":"Uchida"},{"full_name":"Torii, Keiko U","first_name":"Keiko U","last_name":"Torii"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nature Plants","issue":"7"},{"publisher":"ACM","year":"2018","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/783"}],"department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"type":"conference","oa":1,"external_id":{"isi":["000516620100005"]},"day":"01","title":"On the memory hardness of data independent password hashing functions","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"doi":"10.1145/3196494.3196534","oa_version":"Submitted Version","scopus_import":"1","_id":"193","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"quality_controlled":"1","date_created":"2018-12-11T11:45:07Z","isi":1,"author":[{"first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gazi, Peter","first_name":"Peter","last_name":"Gazi"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"last_name":"Klein","first_name":"Karen","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","first_name":"Georg F"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reyzin","first_name":"Lenoid","full_name":"Reyzin, Lenoid"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"last_name":"Rybar","first_name":"Michal","full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","ec_funded":1,"acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","month":"06","page":"51 - 65","date_published":"2018-06-01T00:00:00Z","conference":{"end_date":"2018-06-08","start_date":"2018-06-04","name":"ASIACCS: Asia Conference on Computer and Communications Security ","location":"Incheon, Republic of Korea"},"citation":{"ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i> (pp. 51–65). Incheon, Republic of Korea: ACM. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>","ieee":"J. F. Alwen <i>et al.</i>, “On the memory hardness of data independent password hashing functions,” in <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, Incheon, Republic of Korea, 2018, pp. 51–65.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, ACM, 2018, pp. 51–65, doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>.","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, 51–65. ACM, 2018. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>. ACM; 2018:51-65. doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>"},"abstract":[{"text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.","lang":"eng"}],"publist_id":"7723","date_updated":"2024-11-04T13:52:29Z"},{"title":"Anyonic statistics of quantum impurities in two dimensions","article_processing_charge":"No","arxiv":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/1712.00308","open_access":"1"}],"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2018","oa":1,"day":"15","external_id":{"arxiv":["1712.00308"],"isi":["000436939100007"]},"type":"journal_article","quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"isi":1,"date_created":"2018-12-11T11:45:08Z","language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Submitted Version","_id":"195","doi":"10.1103/PhysRevB.98.045402","month":"07","article_number":"045402","ec_funded":1,"volume":98,"author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"status":"public","publication":"Physical Review B - Condensed Matter and Materials Physics","issue":"4","intvolume":"        98","date_updated":"2025-04-15T06:50:28Z","date_published":"2018-07-15T00:00:00Z","abstract":[{"lang":"eng","text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases."}],"citation":{"ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>.","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4. American Physical Society, 2018.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018).","apa":"Yakaboylu, E., &#38; Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2018;98(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>."},"corr_author":"1"},{"_id":"19544","oa_version":"Published Version","doi":"10.1038/s41420-018-0120-z","OA_place":"publisher","language":[{"iso":"eng"}],"DOAJ_listed":"1","article_type":"original","date_created":"2025-04-11T01:31:42Z","quality_controlled":"1","pmid":1,"external_id":{"pmid":["30455989 "]},"day":"13","oa":1,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41420-018-0120-z"}],"department":[{"_id":"GradSch"},{"_id":"LoSw"}],"publication_status":"published","OA_type":"gold","year":"2018","publisher":"Springer Nature","publication_identifier":{"issn":["2058-7716"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","title":"Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors","abstract":[{"lang":"eng","text":"Medicinal bioinorganic chemistry is a thriving field of drug research for cancer treatment. Transition metal complexes coordinated to essential biological scaffolds represent a highly promising class of compounds for design of novel target-specific therapeutics. We report here the biological evaluation of a novel Isatin-Schiff base derivative and its Cu(II) complex in several tumor cell lines by assessing their effects on cellular metabolism, real-time cell proliferation and induction of apoptosis. Further, the impact of compounds on the p53 protein and expression of its target genes, including MDM2, p21/CDKN1A, and PUMA was evaluated. Results obtained in this study provide further evidence in support of our prior data suggesting the p53-mediated mechanism of action for Isatin-Schiff base derivatives and their complexes and also shed light on potential use of these compounds for stimulation of apoptosis in breast cancer cells via activation of the pro-apoptotic PUMA gene."}],"citation":{"ama":"Bulatov E, Sayarova R, Mingaleeva R, et al. Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. <i>Cell Death Discovery</i>. 2018;4. doi:<a href=\"https://doi.org/10.1038/s41420-018-0120-z\">10.1038/s41420-018-0120-z</a>","chicago":"Bulatov, Emil, Regina Sayarova, Rimma Mingaleeva, Regina Miftakhova, Marina Gomzikova, Iurii Ignatev, Alexey Petukhov, Pavel Davidovich, Albert Rizvanov, and Nickolai A. Barlev. “Isatin-Schiff Base-Copper (II) Complex Induces Cell Death in P53-Positive Tumors.” <i>Cell Death Discovery</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41420-018-0120-z\">https://doi.org/10.1038/s41420-018-0120-z</a>.","ieee":"E. Bulatov <i>et al.</i>, “Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors,” <i>Cell Death Discovery</i>, vol. 4. Springer Nature, 2018.","short":"E. Bulatov, R. Sayarova, R. Mingaleeva, R. Miftakhova, M. Gomzikova, I. Ignatev, A. Petukhov, P. Davidovich, A. Rizvanov, N.A. Barlev, Cell Death Discovery 4 (2018).","mla":"Bulatov, Emil, et al. “Isatin-Schiff Base-Copper (II) Complex Induces Cell Death in P53-Positive Tumors.” <i>Cell Death Discovery</i>, vol. 4, 103, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41420-018-0120-z\">10.1038/s41420-018-0120-z</a>.","apa":"Bulatov, E., Sayarova, R., Mingaleeva, R., Miftakhova, R., Gomzikova, M., Ignatev, I., … Barlev, N. A. (2018). Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. <i>Cell Death Discovery</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41420-018-0120-z\">https://doi.org/10.1038/s41420-018-0120-z</a>","ista":"Bulatov E, Sayarova R, Mingaleeva R, Miftakhova R, Gomzikova M, Ignatev I, Petukhov A, Davidovich P, Rizvanov A, Barlev NA. 2018. Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. Cell Death Discovery. 4, 103."},"has_accepted_license":"1","date_published":"2018-11-13T00:00:00Z","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"},"date_updated":"2025-07-10T11:51:52Z","extern":"1","intvolume":"         4","publication":"Cell Death Discovery","status":"public","author":[{"full_name":"Bulatov, Emil","last_name":"Bulatov","first_name":"Emil"},{"last_name":"Sayarova","first_name":"Regina","full_name":"Sayarova, Regina"},{"full_name":"Mingaleeva, Rimma","first_name":"Rimma","last_name":"Mingaleeva"},{"full_name":"Miftakhova, Regina","first_name":"Regina","last_name":"Miftakhova"},{"last_name":"Gomzikova","first_name":"Marina","full_name":"Gomzikova, Marina"},{"full_name":"Ignatev, Iurii","id":"2ac71786-dc7d-11ea-9b2f-c5ad4b9faff6","first_name":"Iurii","last_name":"Ignatev"},{"full_name":"Petukhov, Alexey","first_name":"Alexey","last_name":"Petukhov"},{"last_name":"Davidovich","first_name":"Pavel","full_name":"Davidovich, Pavel"},{"full_name":"Rizvanov, Albert","last_name":"Rizvanov","first_name":"Albert"},{"last_name":"Barlev","first_name":"Nickolai A.","full_name":"Barlev, Nickolai A."}],"month":"11","volume":4,"ddc":["570"],"article_number":"103"},{"date_updated":"2025-05-19T08:28:40Z","intvolume":"         1","citation":{"apa":"Mosienko, V., Rasooli-Nejad, S., Kishi, K., De Both, M., Jane, D., Huentelman, M. J., … Teschemacher, A. G. (2018). Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. MDPI. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>","short":"V. Mosienko, S. Rasooli-Nejad, K. Kishi, M. De Both, D. Jane, M.J. Huentelman, S. Kasparov, A.G. Teschemacher, Neuroglia 1 (2018) 365–380.","mla":"Mosienko, Valentina, et al. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>, vol. 1, no. 2, MDPI, 2018, pp. 365–80, doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>.","ieee":"V. Mosienko <i>et al.</i>, “Putative receptors underpinning L-Lactate signalling in locus coeruleus,” <i>Neuroglia</i>, vol. 1, no. 2. MDPI, pp. 365–380, 2018.","chicago":"Mosienko, Valentina, Seyed Rasooli-Nejad, Kasumi Kishi, Matt De Both, David Jane, Matt J. Huentelman, Sergey Kasparov, and Anja G. Teschemacher. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>.","ama":"Mosienko V, Rasooli-Nejad S, Kishi K, et al. Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. 2018;1(2):365-380. doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>","ista":"Mosienko V, Rasooli-Nejad S, Kishi K, De Both M, Jane D, Huentelman MJ, Kasparov S, Teschemacher AG. 2018. Putative receptors underpinning L-Lactate signalling in locus coeruleus. Neuroglia. 1(2), 365–380."},"abstract":[{"lang":"eng","text":"The importance of astrocytic l-lactate (LL) for normal functioning of neural circuits such as those regulating learning/memory, sleep/wake state, autonomic homeostasis, or emotional behaviour is being increasingly recognised. l-Lactate can act on neurones as a metabolic or redox substrate, but transmembrane receptor targets are also emerging. A comparative review of the hydroxy-carboxylic acid receptor (HCA1, formerly known as GPR81), Olfactory Receptor Family 51 Subfamily E Member 2 (OR51E2), and orphan receptor GPR4 highlights differences in their LL sensitivity, pharmacology, intracellular coupling, and localisation in the brain. In addition, a putative Gs-coupled receptor on noradrenergic neurones, LLRx, which we previously postulated, remains to be identified. Next-generation sequencing revealed several orphan receptors expressed in locus coeruleus neurones. Screening of a selection of these suggests additional LL-sensitive receptors: GPR180 which inhibits and GPR137 which activates intracellular cyclic AMP signalling in response to LL in a heterologous expression system. To further characterise binding of LL at LLRx, we carried out a structure–activity relationship study which demonstrates that carboxyl and 2-hydroxyl moieties of LL are essential for triggering d-lactate-sensitive noradrenaline release in locus coeruleus, and that the size of the LL binding pocket is limited towards the methyl group position. The evidence accumulating to date suggests that LL acts via multiple receptor targets to modulate distinct brain functions."}],"has_accepted_license":"1","date_published":"2018-12-01T00:00:00Z","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"},"file":[{"checksum":"cadb56618f72edf4703b6a9855e84baa","relation":"main_file","access_level":"open_access","date_created":"2025-05-19T08:20:19Z","creator":"dernst","date_updated":"2025-05-19T08:20:19Z","content_type":"application/pdf","file_size":1909402,"file_id":"19711","success":1,"file_name":"2018_Neuroglia_Mosienko.pdf"}],"page":"365-380","month":"12","acknowledgement":"This work was supported by grants from BBSRC BB/L019396/1, and MRC MR/L020661/1. David Kleinfeld for his gift of CNiFER cells, Lesley Arberry for expert technical support, Andrew Herman for support with FACS sorting.","volume":1,"ddc":["570"],"publication":"Neuroglia","issue":"2","status":"public","author":[{"last_name":"Mosienko","first_name":"Valentina","full_name":"Mosienko, Valentina"},{"last_name":"Rasooli-Nejad","first_name":"Seyed","full_name":"Rasooli-Nejad, Seyed"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","first_name":"Kasumi","last_name":"Kishi"},{"last_name":"De Both","first_name":"Matt","full_name":"De Both, Matt"},{"full_name":"Jane, David","last_name":"Jane","first_name":"David"},{"last_name":"Huentelman","first_name":"Matt J.","full_name":"Huentelman, Matt J."},{"last_name":"Kasparov","first_name":"Sergey","full_name":"Kasparov, Sergey"},{"full_name":"Teschemacher, Anja G.","last_name":"Teschemacher","first_name":"Anja G."}],"date_created":"2025-05-18T22:02:51Z","quality_controlled":"1","_id":"19706","oa_version":"Published Version","scopus_import":"1","doi":"10.3390/neuroglia1020025","file_date_updated":"2025-05-19T08:20:19Z","OA_place":"publisher","language":[{"iso":"eng"}],"DOAJ_listed":"1","article_type":"original","publication_identifier":{"eissn":["2571-6980"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","title":"Putative receptors underpinning L-Lactate signalling in locus coeruleus","day":"01","oa":1,"type":"journal_article","department":[{"_id":"AnKi"}],"OA_type":"gold","publication_status":"published","year":"2018","publisher":"MDPI"},{"author":[{"first_name":"Tomoaki","last_name":"Nishiyama","full_name":"Nishiyama, Tomoaki"},{"full_name":"Sakayama, Hidetoshi","last_name":"Sakayama","first_name":"Hidetoshi"},{"last_name":"De Vries","first_name":"Jan","full_name":"De Vries, Jan"},{"first_name":"Henrik","last_name":"Buschmann","full_name":"Buschmann, Henrik"},{"last_name":"Saint Marcoux","first_name":"Denis","full_name":"Saint Marcoux, Denis"},{"full_name":"Ullrich, Kristian","first_name":"Kristian","last_name":"Ullrich"},{"full_name":"Haas, Fabian","first_name":"Fabian","last_name":"Haas"},{"full_name":"Vanderstraeten, Lisa","first_name":"Lisa","last_name":"Vanderstraeten"},{"full_name":"Becker, Dirk","first_name":"Dirk","last_name":"Becker"},{"full_name":"Lang, Daniel","first_name":"Daniel","last_name":"Lang"},{"last_name":"Vosolsobě","first_name":"Stanislav","full_name":"Vosolsobě, Stanislav"},{"full_name":"Rombauts, Stephane","last_name":"Rombauts","first_name":"Stephane"},{"last_name":"Wilhelmsson","first_name":"Per","full_name":"Wilhelmsson, Per"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"first_name":"Alexander","last_name":"Heyl","full_name":"Heyl, Alexander"},{"full_name":"Rümpler, Florian","first_name":"Florian","last_name":"Rümpler"},{"full_name":"Calderón Villalobos, Luz","last_name":"Calderón Villalobos","first_name":"Luz"},{"last_name":"Clay","first_name":"John","full_name":"Clay, John"},{"last_name":"Skokan","first_name":"Roman","full_name":"Skokan, Roman"},{"first_name":"Atsushi","last_name":"Toyoda","full_name":"Toyoda, Atsushi"},{"first_name":"Yutaka","last_name":"Suzuki","full_name":"Suzuki, Yutaka"},{"full_name":"Kagoshima, Hiroshi","first_name":"Hiroshi","last_name":"Kagoshima"},{"last_name":"Schijlen","first_name":"Elio","full_name":"Schijlen, Elio"},{"first_name":"Navindra","last_name":"Tajeshwar","full_name":"Tajeshwar, Navindra"},{"full_name":"Catarino, Bruno","first_name":"Bruno","last_name":"Catarino"},{"full_name":"Hetherington, Alexander","first_name":"Alexander","last_name":"Hetherington"},{"full_name":"Saltykova, Assia","first_name":"Assia","last_name":"Saltykova"},{"full_name":"Bonnot, Clemence","first_name":"Clemence","last_name":"Bonnot"},{"last_name":"Breuninger","first_name":"Holger","full_name":"Breuninger, Holger"},{"full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini","last_name":"Symeonidi"},{"full_name":"Radhakrishnan, Guru","first_name":"Guru","last_name":"Radhakrishnan"},{"full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh","first_name":"Filip"},{"full_name":"Deforce, Dieter","last_name":"Deforce","first_name":"Dieter"},{"first_name":"Caren","last_name":"Chang","full_name":"Chang, Caren"},{"full_name":"Karol, Kenneth","last_name":"Karol","first_name":"Kenneth"},{"first_name":"Rainer","last_name":"Hedrich","full_name":"Hedrich, Rainer"},{"full_name":"Ulvskov, Peter","first_name":"Peter","last_name":"Ulvskov"},{"last_name":"Glöckner","first_name":"Gernot","full_name":"Glöckner, Gernot"},{"last_name":"Delwiche","first_name":"Charles","full_name":"Delwiche, Charles"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Van De Peer","first_name":"Yves","full_name":"Van De Peer, Yves"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beilby, Mary","first_name":"Mary","last_name":"Beilby"},{"full_name":"Dolan, Liam","last_name":"Dolan","first_name":"Liam"},{"last_name":"Kohara","first_name":"Yuji","full_name":"Kohara, Yuji"},{"last_name":"Sugano","first_name":"Sumio","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","last_name":"Fujiyama","first_name":"Asao"},{"first_name":"Pierre Marc","last_name":"Delaux","full_name":"Delaux, Pierre Marc"},{"first_name":"Marcel","last_name":"Quint","full_name":"Quint, Marcel"},{"last_name":"Theissen","first_name":"Gunter","full_name":"Theissen, Gunter"},{"full_name":"Hagemann, Martin","first_name":"Martin","last_name":"Hagemann"},{"full_name":"Harholt, Jesper","last_name":"Harholt","first_name":"Jesper"},{"full_name":"Dunand, Christophe","first_name":"Christophe","last_name":"Dunand"},{"last_name":"Zachgo","first_name":"Sabine","full_name":"Zachgo, Sabine"},{"first_name":"Jane","last_name":"Langdale","full_name":"Langdale, Jane"},{"full_name":"Maumus, Florian","last_name":"Maumus","first_name":"Florian"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"},{"first_name":"Sven B","last_name":"Gould","full_name":"Gould, Sven B"},{"last_name":"Rensing","first_name":"Stefan","full_name":"Rensing, Stefan"}],"status":"public","issue":"2","publication":"Cell","volume":174,"ec_funded":1,"acknowledgement":"In-Data-Review","month":"07","page":"448 - 464.e24","date_published":"2018-07-12T00:00:00Z","abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"citation":{"short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","ieee":"T. Nishiyama <i>et al.</i>, “The Chara genome: Secondary complexity and implications for plant terrestrialization,” <i>Cell</i>, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. 2018;174(2):448-464.e24. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>.","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24."},"intvolume":"       174","publist_id":"7774","date_updated":"2025-04-14T07:45:02Z","publisher":"Cell Press","year":"2018","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417"}],"department":[{"_id":"JiFr"}],"type":"journal_article","oa":1,"external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"pmid":1,"day":"12","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2018.06.033","scopus_import":"1","oa_version":"Published Version","_id":"148","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"quality_controlled":"1","date_created":"2018-12-11T11:44:53Z","isi":1},{"date_updated":"2023-09-12T07:44:37Z","intvolume":"       560","abstract":[{"lang":"eng","text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1."}],"citation":{"ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512."},"date_published":"2018-08-29T00:00:00Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"page":"509–512","month":"08","volume":560,"issue":"7719","publication":"Nature","status":"public","author":[{"full_name":"Dick, Robert","last_name":"Dick","first_name":"Robert"},{"first_name":"Kaneil K","last_name":"Zadrozny","full_name":"Zadrozny, Kaneil K"},{"full_name":"Xu, Chaoyi","first_name":"Chaoyi","last_name":"Xu"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian"},{"full_name":"Lyddon, Terri D","last_name":"Lyddon","first_name":"Terri D"},{"full_name":"Ricana, Clifton L","first_name":"Clifton L","last_name":"Ricana"},{"full_name":"Wagner, Jonathan M","last_name":"Wagner","first_name":"Jonathan M"},{"full_name":"Perilla, Juan R","last_name":"Perilla","first_name":"Juan R"},{"full_name":"Ganser, Pornillos Barbie K","first_name":"Pornillos Barbie K","last_name":"Ganser"},{"full_name":"Johnson, Marc C","first_name":"Marc C","last_name":"Johnson"},{"full_name":"Pornillos, Owen","last_name":"Pornillos","first_name":"Owen"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"}],"isi":1,"date_created":"2018-12-11T11:44:53Z","quality_controlled":"1","_id":"150","oa_version":"Submitted Version","scopus_import":"1","doi":"10.1038/s41586-018-0396-4","language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"eissn":["1476-4687"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Inositol phosphates are assembly co-factors for HIV-1","pmid":1,"day":"29","external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"oa":1,"type":"journal_article","department":[{"_id":"FlSc"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/"}],"publication_status":"published","year":"2018","publisher":"Nature Publishing Group"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_published":"2018-07-26T00:00:00Z","has_accepted_license":"1","citation":{"apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867."},"abstract":[{"lang":"eng","text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context."}],"intvolume":"        28","publist_id":"7769","date_updated":"2023-09-13T08:51:56Z","author":[{"full_name":"Fiedorczuk, Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol","last_name":"Fiedorczuk"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publication":"Trends in Cell Biology","issue":"10","ddc":["572"],"volume":28,"month":"07","page":"835 - 867","file":[{"content_type":"application/pdf","file_size":2185385,"file_id":"6994","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","date_created":"2019-11-07T12:55:20Z","access_level":"open_access","date_updated":"2020-07-14T12:45:00Z","creator":"lsazanov"}],"article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:00Z","doi":"10.1016/j.tcb.2018.06.006","oa_version":"Submitted Version","scopus_import":"1","_id":"152","quality_controlled":"1","date_created":"2018-12-11T11:44:54Z","isi":1,"publisher":"Elsevier","publication_status":"published","year":"2018","department":[{"_id":"LeSa"}],"type":"journal_article","oa":1,"day":"26","external_id":{"isi":["000445118200007"]},"title":"Mammalian mitochondrial complex I structure and disease causing mutations","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"day":"27","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"pmid":1,"type":"book_chapter","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"publisher":"Academic Press","year":"2018","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0091-679X"]},"title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","article_processing_charge":"No","scopus_import":"1","oa_version":"None","_id":"153","doi":"10.1016/bs.mcb.2018.07.004","language":[{"iso":"eng"}],"isi":1,"date_created":"2018-12-11T11:44:54Z","quality_controlled":"1","publication":"Methods in Cell Biology","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","first_name":"Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz"},{"full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","last_name":"Reversat","first_name":"Anne"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","last_name":"Leithner","orcid":"0000-0002-1073-744X"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"status":"public","page":"79 - 91","month":"07","volume":147,"citation":{"ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>.","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>"},"abstract":[{"text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters.","lang":"eng"}],"date_published":"2018-07-27T00:00:00Z","date_updated":"2025-07-10T11:51:09Z","publist_id":"7768","intvolume":"       147"},{"status":"public","author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","first_name":"Arseniy"},{"full_name":"Petrunin, Anton","first_name":"Anton","last_name":"Petrunin"}],"publication":"Mathematical Intelligencer","issue":"3","volume":40,"month":"09","page":"26 - 31","date_published":"2018-09-01T00:00:00Z","citation":{"mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” <i>Mathematical Intelligencer</i>, vol. 40, no. 3. Springer, pp. 26–31, 2018.","apa":"Akopyan, A., &#38; Petrunin, A. (2018). Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. Springer. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. 2018;40(3):26-31. doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31."},"abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"intvolume":"        40","publist_id":"7948","date_updated":"2023-09-13T08:49:16Z","publication_status":"published","year":"2018","publisher":"Springer","department":[{"_id":"HeEd"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"type":"journal_article","external_id":{"isi":["000444141200005"],"arxiv":["1702.05172"]},"day":"01","oa":1,"article_processing_charge":"No","title":"Long geodesics on convex surfaces","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00283-018-9795-5","_id":"106","oa_version":"Preprint","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T11:44:40Z","isi":1},{"status":"public","author":[{"first_name":"Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"first_name":"Alexey","last_name":"Balitskiy","full_name":"Balitskiy, Alexey"},{"full_name":"Grigorev, Mikhail","first_name":"Mikhail","last_name":"Grigorev"}],"issue":"4","publication":"Discrete & Computational Geometry","volume":59,"ec_funded":1,"ddc":["516","000"],"month":"06","page":"1001-1009","file":[{"file_size":482518,"content_type":"application/pdf","file_name":"2018_DiscreteComp_Akopyan.pdf","success":1,"file_id":"5844","relation":"main_file","date_updated":"2019-01-18T09:27:36Z","creator":"dernst","date_created":"2019-01-18T09:27:36Z","access_level":"open_access"}],"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"},"date_published":"2018-06-01T00:00:00Z","has_accepted_license":"1","corr_author":"1","citation":{"ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete &#38; Computational Geometry. 59(4), 1001–1009.","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. 2018;59(4):1001-1009. doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>.","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete &#38; Computational Geometry 59 (2018) 1001–1009.","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>.","apa":"Akopyan, A., Balitskiy, A., &#38; Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>"},"abstract":[{"lang":"eng","text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets."}],"intvolume":"        59","publist_id":"6324","date_updated":"2025-04-15T06:50:01Z","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"HeEd"}],"type":"journal_article","external_id":{"isi":["000432205500011"]},"day":"01","oa":1,"article_processing_charge":"Yes (via OA deal)","title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","file_date_updated":"2019-01-18T09:27:36Z","language":[{"iso":"eng"}],"doi":"10.1007/s00454-017-9883-x","_id":"1064","oa_version":"Published Version","scopus_import":"1","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"quality_controlled":"1","date_created":"2018-12-11T11:49:57Z","isi":1},{"intvolume":"        65","publist_id":"7947","date_updated":"2025-04-14T07:22:06Z","date_published":"2018-08-01T00:00:00Z","citation":{"short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” <i>Journal of the ACM</i>, vol. 65, no. 4, 20, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>.","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” <i>Journal of the ACM</i>, vol. 65, no. 4. ACM, 2018.","apa":"Dziembowski, S., Pietrzak, K. Z., &#38; Wichs, D. (2018). Non-malleable codes. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. <i>Journal of the ACM</i>. 2018;65(4). doi:<a href=\"https://doi.org/10.1145/3178432\">10.1145/3178432</a>","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” <i>Journal of the ACM</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3178432\">https://doi.org/10.1145/3178432</a>.","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20."},"abstract":[{"text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.","lang":"eng"}],"article_number":"20","volume":65,"ec_funded":1,"month":"08","author":[{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"status":"public","issue":"4","publication":"Journal of the ACM","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"},{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668"}],"quality_controlled":"1","date_created":"2018-12-11T11:44:40Z","isi":1,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1145/3178432","scopus_import":"1","oa_version":"Preprint","_id":"107","title":"Non-malleable codes","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"ACM","publication_status":"published","year":"2018","department":[{"_id":"KrPi"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2009/608"}],"type":"journal_article","oa":1,"external_id":{"isi":["000442938200004"]},"day":"01"},{"abstract":[{"text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes.","lang":"eng"}],"citation":{"short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","mla":"Obremski, Marciej, and Maciej Skórski. <i>Inverted Leftover Hash Lemma</i>. Vol. 2018, IEEE, 2018, doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>.","apa":"Obremski, M., &#38; Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:<a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">10.1109/ISIT.2018.8437654</a>","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. <a href=\"https://doi.org/10.1109/ISIT.2018.8437654\">https://doi.org/10.1109/ISIT.2018.8437654</a>.","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018."},"conference":{"name":"ISIT: International Symposium on Information Theory","location":"Vail, CO, USA","start_date":"2018-06-17 ","end_date":"2018-06-22"},"date_published":"2018-08-16T00:00:00Z","date_updated":"2023-09-13T08:23:18Z","publist_id":"7946","intvolume":"      2018","alternative_title":["ISIT Proceedings"],"status":"public","author":[{"last_name":"Obremski","first_name":"Marciej","full_name":"Obremski, Marciej"},{"full_name":"Skorski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skorski","first_name":"Maciej"}],"month":"08","volume":2018,"_id":"108","oa_version":"Submitted Version","scopus_import":"1","doi":"10.1109/ISIT.2018.8437654","language":[{"iso":"eng"}],"isi":1,"date_created":"2018-12-11T11:44:40Z","quality_controlled":"1","external_id":{"isi":["000448139300368"]},"day":"16","oa":1,"type":"conference","department":[{"_id":"KrPi"}],"main_file_link":[{"url":"https://eprint.iacr.org/2017/507","open_access":"1"}],"year":"2018","publication_status":"published","publisher":"IEEE","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Inverted leftover hash lemma"},{"page":"203-220","editor":[{"last_name":"Czelakowski","first_name":"J","full_name":"Czelakowski, J"}],"month":"03","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","volume":16,"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","status":"public","author":[{"last_name":"Kazda","first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr"},{"full_name":"Kozik, Marcin","last_name":"Kozik","first_name":"Marcin"},{"full_name":"McKenzie, Ralph","last_name":"McKenzie","first_name":"Ralph"},{"first_name":"Matthew","last_name":"Moore","full_name":"Moore, Matthew"}],"date_updated":"2024-10-09T21:01:50Z","intvolume":"        16","abstract":[{"lang":"eng","text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k."}],"citation":{"apa":"Kazda, A., Kozik, M., McKenzie, R., &#38; Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i> (Vol. 16, pp. 203–220). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220."},"corr_author":"1","date_published":"2018-03-21T00:00:00Z","arxiv":1,"publication_identifier":{"issn":["2211-2758"],"eisbn":["9783319747729"],"eissn":["2211-2766"],"isbn":["9783319747712"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Absorption and directed Jónsson terms","day":"21","external_id":{"arxiv":["1502.01072"]},"oa":1,"type":"book_chapter","department":[{"_id":"VlKo"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"year":"2018","publication_status":"published","publisher":"Springer Nature","place":"Cham","date_created":"2022-03-18T10:30:32Z","quality_controlled":"1","_id":"10864","scopus_import":"1","oa_version":"Preprint","doi":"10.1007/978-3-319-74772-9_7","series_title":"OCTR","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["2041-2649"],"eissn":["2041-2657"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","day":"01","pmid":1,"external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"oa":1,"type":"journal_article","department":[{"_id":"CaHe"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bfgp/ely007"}],"year":"2018","publication_status":"published","publisher":"Oxford University Press","isi":1,"date_created":"2022-03-18T12:40:35Z","quality_controlled":"1","_id":"10880","scopus_import":"1","oa_version":"Published Version","doi":"10.1093/bfgp/ely007","language":[{"iso":"eng"}],"article_type":"original","page":"329-338","month":"09","volume":17,"acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","issue":"5","publication":"Briefings in Functional Genomics","status":"public","author":[{"full_name":"Yuuta, Moriyama","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2853-8051","last_name":"Yuuta","first_name":"Moriyama"},{"full_name":"Koshiba-Takeuchi, Kazuko","last_name":"Koshiba-Takeuchi","first_name":"Kazuko"}],"date_updated":"2024-10-09T21:01:52Z","intvolume":"        17","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"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."}],"citation":{"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>","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>.","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","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.","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>.","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."},"corr_author":"1","date_published":"2018-09-01T00:00:00Z"},{"intvolume":"        69","keyword":["Plant Science","Physiology"],"date_updated":"2025-04-15T07:48:01Z","date_published":"2018-04-13T00:00:00Z","citation":{"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.","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.","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>.","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.","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>","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>."},"abstract":[{"lang":"eng","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."}],"month":"04","volume":69,"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. ","ec_funded":1,"page":"2367-2378","author":[{"first_name":"Taraka Ramji","last_name":"Moturu","full_name":"Moturu, Taraka Ramji"},{"full_name":"Thula, Sravankumar","first_name":"Sravankumar","last_name":"Thula"},{"last_name":"Singh","first_name":"Ravi Kumar","full_name":"Singh, Ravi Kumar"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"last_name":"Vařeková","first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu"}],"status":"public","publication":"Journal of Experimental Botany","issue":"9","quality_controlled":"1","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"isi":1,"date_created":"2022-03-18T12:43:22Z","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","oa_version":"None","_id":"10881","doi":"10.1093/jxb/ery097","title":"Molecular evolution and diversification of the SMXL gene family","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","year":"2018","publication_status":"published","external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"pmid":1,"day":"13","type":"journal_article"},{"page":"9175-9184","month":"12","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","author":[{"full_name":"Uijlings, Jasper","first_name":"Jasper","last_name":"Uijlings"},{"last_name":"Konyushkova","first_name":"Ksenia","full_name":"Konyushkova, Ksenia"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"last_name":"Ferrari","first_name":"Vittorio","full_name":"Ferrari, Vittorio"}],"status":"public","date_updated":"2024-10-09T21:02:26Z","corr_author":"1","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"},"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.","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>.","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>","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>","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.","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.","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>."},"abstract":[{"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.","lang":"eng"}],"date_published":"2018-12-17T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"isbn":["9781538664209"],"eissn":["2575-7075"]},"arxiv":1,"title":"Learning intelligent dialogs for bounding box annotation","article_processing_charge":"No","type":"conference","oa":1,"day":"17","external_id":{"arxiv":["1712.08087"],"isi":["000457843609036"]},"publisher":"IEEE","year":"2018","publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"department":[{"_id":"ChLa"}],"date_created":"2022-03-18T12:45:09Z","isi":1,"quality_controlled":"1","doi":"10.1109/cvpr.2018.00956","scopus_import":"1","oa_version":"Preprint","_id":"10882","language":[{"iso":"eng"}]},{"department":[{"_id":"KrCh"}],"publisher":"EasyChair","publication_status":"published","year":"2018","oa":1,"day":"23","external_id":{"arxiv":["1909.04983"]},"type":"conference","title":"Quasipolynomial set-based symbolic algorithms for parity games","article_processing_charge":"No","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2398-7340"]},"file_date_updated":"2022-05-17T07:51:08Z","language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","_id":"10883","doi":"10.29007/5z5k","quality_controlled":"1","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","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"}],"date_created":"2022-03-18T12:46:32Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Dvořák, Wolfgang","first_name":"Wolfgang","last_name":"Dvořák"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"status":"public","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","alternative_title":["EPiC Series in Computing"],"month":"10","ddc":["000"],"ec_funded":1,"volume":57,"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.","file":[{"file_size":720893,"content_type":"application/pdf","file_name":"2018_EPiCs_Chatterjee.pdf","success":1,"file_id":"11392","relation":"main_file","checksum":"1229aa8640bd6db610c85decf2265480","date_updated":"2022-05-17T07:51:08Z","creator":"dernst","date_created":"2022-05-17T07:51:08Z","access_level":"open_access"}],"page":"233-253","date_published":"2018-10-23T00:00:00Z","conference":{"start_date":"2018-11-17","end_date":"2018-11-21","location":"Awassa, Ethiopia","name":"LPAR: Logic for Programming, Artificial Intelligence and Reasoning"},"citation":{"apa":"Chatterjee, K., Dvořák, W., Henzinger, M., &#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>","short":"K. Chatterjee, W. Dvořák, M. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","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>.","ieee":"K. Chatterjee, W. Dvořák, M. 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.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika 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>.","ama":"Chatterjee K, Dvořák W, Henzinger M, 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>","ista":"Chatterjee K, Dvořák W, Henzinger M, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253."},"abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","intvolume":"        57","date_updated":"2025-07-10T11:50:02Z"}]