[{"article_type":"original","date_updated":"2023-10-17T11:51:06Z","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"type":"journal_article","date_published":"2018-08-28T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:11Z","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","intvolume":"        35","page":"2669 - 2684","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>.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","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.","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>","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>.","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>","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."},"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"issue":"11","publist_id":"8036","volume":35,"fulldoi":"https://doi.org/10.1093/molbev/msy163","doi":"10.1093/molbev/msy163","publisher":"Oxford University Press","publication_identifier":{"issn":["0737-4038"]},"day":"28","publication":"Molecular Biology and Evolution","status":"public","_id":"19","month":"08","year":"2018","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","isi":1,"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."}],"pmid":1,"author":[{"full_name":"Palmer, Adam","first_name":"Adam","last_name":"Palmer"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}]},{"publisher":"Wiley","doi":"10.1002/jez.b.22824","fulldoi":"https://doi.org/10.1002/jez.b.22824","day":"11","year":"2018","_id":"190","status":"public","month":"07","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","scopus_import":"1","oa":1,"article_processing_charge":"No","isi":1,"abstract":[{"lang":"eng","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."}],"author":[{"first_name":"Mark","full_name":"Harrison, Mark","last_name":"Harrison"},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"first_name":"Lucas","full_name":"Kremer, Lucas","last_name":"Kremer"},{"first_name":"Guillem","full_name":"Ylla, Guillem","last_name":"Ylla"},{"full_name":"Belles, Xavier","first_name":"Xavier","last_name":"Belles"},{"last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich","first_name":"Erich"},{"last_name":"Huylmans","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"full_name":"Puilachs, Maria","first_name":"Maria","last_name":"Puilachs"},{"full_name":"Richards, Stephen","first_name":"Stephen","last_name":"Richards"},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"}],"pmid":1,"article_type":"original","publication_status":"published","department":[{"_id":"BeVi"}],"date_updated":"2023-09-11T13:59:54Z","date_published":"2018-07-11T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"       330","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","date_created":"2018-12-11T11:45:06Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}],"external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"citation":{"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>.","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>","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>","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>.","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."},"page":"254-264","publist_id":"7730","volume":330},{"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"date_updated":"2023-09-15T12:11:03Z","article_type":"original","quality_controlled":"1","intvolume":"         4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:45:07Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"date_published":"2018-06-25T00:00:00Z","type":"journal_article","issue":"7","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"page":"453 - 459","citation":{"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>.","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>.","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.","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.","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."},"volume":4,"publist_id":"7728","day":"25","publisher":"Springer Nature","doi":"10.1038/s41477-018-0190-1","fulldoi":"https://doi.org/10.1038/s41477-018-0190-1","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","scopus_import":"1","oa":1,"article_processing_charge":"No","year":"2018","_id":"192","status":"public","month":"06","publication":"Nature Plants","isi":1,"author":[{"last_name":"Fendrych","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas"},{"last_name":"Akhmanova","orcid":"0000-0003-1522-3162","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","full_name":"Akhmanova, Maria"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"first_name":"Matous","full_name":"Glanc, Matous","last_name":"Glanc"},{"full_name":"Hagihara, Shinya","first_name":"Shinya","last_name":"Hagihara"},{"first_name":"Koji","full_name":"Takahashi, Koji","last_name":"Takahashi"},{"full_name":"Uchida, Naoyuki","first_name":"Naoyuki","last_name":"Uchida"},{"full_name":"Torii, Keiko U","first_name":"Keiko U","last_name":"Torii"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"pmid":1,"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"}]},"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"}]},{"ec_funded":1,"external_id":{"isi":["000516620100005"]},"page":"51 - 65","citation":{"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>.","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>","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>.","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.","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>","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.","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."},"main_file_link":[{"url":"https://eprint.iacr.org/2016/783","open_access":"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.","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"publist_id":"7723","date_updated":"2024-11-04T13:52:29Z","publication_status":"published","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:45:07Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","date_published":"2018-06-01T00:00:00Z","isi":1,"author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"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"},{"first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen","last_name":"Klein"},{"orcid":"0000-0002-8882-5116","first_name":"Georg F","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"full_name":"Reyzin, Lenoid","first_name":"Lenoid","last_name":"Reyzin"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal","first_name":"Michal","last_name":"Rybar"}],"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"}],"day":"01","fulldoi":"https://doi.org/10.1145/3196494.3196534","publisher":"ACM","doi":"10.1145/3196494.3196534","oa":1,"article_processing_charge":"No","title":"On the memory hardness of data independent password hashing functions","scopus_import":"1","conference":{"location":"Incheon, Republic of Korea","name":"ASIACCS: Asia Conference on Computer and Communications Security ","end_date":"2018-06-08","start_date":"2018-06-04"},"publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","year":"2018","_id":"193","month":"06","status":"public"},{"abstract":[{"text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.","lang":"eng"}],"pmid":1,"author":[{"last_name":"Liutkeviciute","first_name":"Zita","full_name":"Liutkeviciute, Zita"},{"last_name":"Gil Mansilla","first_name":"Esther","full_name":"Gil Mansilla, Esther"},{"last_name":"Eder","first_name":"Thomas","full_name":"Eder, Thomas"},{"first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"last_name":"Giulia Di Giglio","full_name":"Giulia Di Giglio, Maria","first_name":"Maria"},{"last_name":"Muratspahić","full_name":"Muratspahić, Edin","first_name":"Edin"},{"full_name":"Grebien, Florian","first_name":"Florian","last_name":"Grebien"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"last_name":"Muttenthaler","first_name":"Markus","full_name":"Muttenthaler, Markus"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Christian","full_name":"Gruber, Christian","last_name":"Gruber"}],"isi":1,"publication":"The FASEB Journal","year":"2018","_id":"194","month":"11","status":"public","oa":1,"article_processing_charge":"No","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","scopus_import":"1","fulldoi":"https://doi.org/10.1096/fj.201800443","ddc":["570"],"publisher":"FASEB","doi":"10.1096/fj.201800443","publication_identifier":{"issn":["0892-6638"]},"day":"29","publist_id":"7721","volume":32,"project":[{"name":"Individual function and social role of oxytocin-like neuropeptides in ants","_id":"25E3D34E-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"page":"6808-6821","citation":{"chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>. FASEB, 2018. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>.","ieee":"Z. Liutkeviciute <i>et al.</i>, “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” <i>The FASEB Journal</i>, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. 2018;32(12):6808-6821. doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. FASEB. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>."},"main_file_link":[{"url":" https://doi.org/10.1096/fj.201800443","open_access":"1"}],"issue":"12","type":"journal_article","date_published":"2018-11-29T00:00:00Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:45:08Z","language":[{"iso":"eng"}],"intvolume":"        32","quality_controlled":"1","article_type":"original","date_updated":"2026-06-18T18:15:11Z","publication_status":"published","department":[{"_id":"SyCr"}]},{"article_type":"original","publication_status":"published","extern":"1","date_updated":"2025-07-10T11:51:49Z","date_published":"2018-09-28T00:00:00Z","type":"journal_article","quality_controlled":"1","intvolume":"       125","arxiv":1,"language":[{"iso":"eng"}],"date_created":"2025-04-05T10:51:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1706.05919","open_access":"1"}],"page":"689-703","citation":{"apa":"Chan, S. (2018). Rational right triangles of a given area. <i>The American Mathematical Monthly</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00029890.2018.1495491\">https://doi.org/10.1080/00029890.2018.1495491</a>","mla":"Chan, Stephanie. “Rational Right Triangles of a given Area.” <i>The American Mathematical Monthly</i>, vol. 125, no. 8, Taylor &#38; Francis, 2018, pp. 689–703, doi:<a href=\"https://doi.org/10.1080/00029890.2018.1495491\">10.1080/00029890.2018.1495491</a>.","ista":"Chan S. 2018. Rational right triangles of a given area. The American Mathematical Monthly. 125(8), 689–703.","ama":"Chan S. Rational right triangles of a given area. <i>The American Mathematical Monthly</i>. 2018;125(8):689-703. doi:<a href=\"https://doi.org/10.1080/00029890.2018.1495491\">10.1080/00029890.2018.1495491</a>","short":"S. Chan, The American Mathematical Monthly 125 (2018) 689–703.","ieee":"S. Chan, “Rational right triangles of a given area,” <i>The American Mathematical Monthly</i>, vol. 125, no. 8. Taylor &#38; Francis, pp. 689–703, 2018.","chicago":"Chan, Stephanie. “Rational Right Triangles of a given Area.” <i>The American Mathematical Monthly</i>. Taylor &#38; Francis, 2018. <a href=\"https://doi.org/10.1080/00029890.2018.1495491\">https://doi.org/10.1080/00029890.2018.1495491</a>."},"external_id":{"arxiv":["1706.05919"]},"issue":"8","volume":125,"OA_place":"repository","doi":"10.1080/00029890.2018.1495491","publisher":"Taylor & Francis","fulldoi":"https://doi.org/10.1080/00029890.2018.1495491","day":"28","publication_identifier":{"eissn":["1930-0972"],"issn":["0002-9890"]},"_id":"19494","month":"09","status":"public","year":"2018","publication":"The American Mathematical Monthly","scopus_import":"1","title":"Rational right triangles of a given area","article_processing_charge":"No","oa":1,"OA_type":"green","abstract":[{"lang":"eng","text":"Starting from any given rational-sided, right triangle, for example, the (3,4,5)-triangle with area 6, we use Euclidean geometry to show that there are infinitely many other rational-sided, right triangles of the same area. We show further that the set of all such triangles of a given area is finitely generated under our geometric construction. Such areas are known as “congruent numbers” and have a rich history in which all the results in this article have been proved and far more. Yet, as far as we can tell, this seems to be the first exploration using this kind of geometric technique."}],"author":[{"orcid":"0000-0001-8467-4106","first_name":"Yik Tung","full_name":"Chan, Yik Tung","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1","last_name":"Chan"}]},{"title":"Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors","oa":1,"article_processing_charge":"Yes","year":"2018","_id":"19544","status":"public","month":"11","publication":"Cell Death Discovery","DOAJ_listed":"1","license":"https://creativecommons.org/licenses/by/4.0/","day":"13","publication_identifier":{"issn":["2058-7716"]},"publisher":"Springer Nature","OA_place":"publisher","doi":"10.1038/s41420-018-0120-z","fulldoi":"https://doi.org/10.1038/s41420-018-0120-z","ddc":["570"],"author":[{"last_name":"Bulatov","full_name":"Bulatov, Emil","first_name":"Emil"},{"first_name":"Regina","full_name":"Sayarova, Regina","last_name":"Sayarova"},{"first_name":"Rimma","full_name":"Mingaleeva, Rimma","last_name":"Mingaleeva"},{"last_name":"Miftakhova","full_name":"Miftakhova, Regina","first_name":"Regina"},{"last_name":"Gomzikova","first_name":"Marina","full_name":"Gomzikova, Marina"},{"id":"2ac71786-dc7d-11ea-9b2f-c5ad4b9faff6","full_name":"Ignatev, Iurii","first_name":"Iurii","last_name":"Ignatev"},{"last_name":"Petukhov","first_name":"Alexey","full_name":"Petukhov, Alexey"},{"last_name":"Davidovich","first_name":"Pavel","full_name":"Davidovich, Pavel"},{"first_name":"Albert","full_name":"Rizvanov, Albert","last_name":"Rizvanov"},{"first_name":"Nickolai A.","full_name":"Barlev, Nickolai A.","last_name":"Barlev"}],"pmid":1,"abstract":[{"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.","lang":"eng"}],"article_number":"103","OA_type":"gold","quality_controlled":"1","intvolume":"         4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2025-04-11T01:31:42Z","language":[{"iso":"eng"}],"date_published":"2018-11-13T00:00:00Z","has_accepted_license":"1","type":"journal_article","department":[{"_id":"GradSch"},{"_id":"LoSw"}],"extern":"1","publication_status":"published","date_updated":"2025-07-10T11:51:52Z","article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"volume":4,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41420-018-0120-z"}],"external_id":{"pmid":["30455989 "]},"citation":{"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).","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.","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>","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>.","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>","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.","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>."}},{"article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"success":1,"content_type":"application/pdf","file_name":"2018_Neuroglia_Mosienko.pdf","file_id":"19711","checksum":"cadb56618f72edf4703b6a9855e84baa","relation":"main_file","date_updated":"2025-05-19T08:20:19Z","access_level":"open_access","file_size":1909402,"creator":"dernst","date_created":"2025-05-19T08:20:19Z"}],"publication_status":"published","department":[{"_id":"AnKi"}],"date_updated":"2025-05-19T08:28:40Z","date_published":"2018-12-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","quality_controlled":"1","intvolume":"         1","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2025-05-18T22:02:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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.","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.","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>.","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>","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."},"page":"365-380","issue":"2","volume":1,"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.","doi":"10.3390/neuroglia1020025","file_date_updated":"2025-05-19T08:20:19Z","OA_place":"publisher","publisher":"MDPI","fulldoi":"https://doi.org/10.3390/neuroglia1020025","ddc":["570"],"day":"01","publication_identifier":{"eissn":["2571-6980"]},"_id":"19706","month":"12","status":"public","year":"2018","DOAJ_listed":"1","publication":"Neuroglia","scopus_import":"1","title":"Putative receptors underpinning L-Lactate signalling in locus coeruleus","article_processing_charge":"Yes","oa":1,"OA_type":"gold","abstract":[{"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.","lang":"eng"}],"author":[{"last_name":"Mosienko","first_name":"Valentina","full_name":"Mosienko, Valentina"},{"last_name":"Rasooli-Nejad","first_name":"Seyed","full_name":"Rasooli-Nejad, Seyed"},{"last_name":"Kishi","first_name":"Kasumi","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Both","full_name":"De Both, Matt","first_name":"Matt"},{"first_name":"David","full_name":"Jane, David","last_name":"Jane"},{"last_name":"Huentelman","full_name":"Huentelman, Matt J.","first_name":"Matt J."},{"full_name":"Kasparov, Sergey","first_name":"Sergey","last_name":"Kasparov"},{"full_name":"Teschemacher, Anja G.","first_name":"Anja G.","last_name":"Teschemacher"}]},{"publication":"Optics Letters","_id":"435","month":"02","status":"public","year":"2018","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Coherent-perfect-absorber and laser for bound states in a continuum","fulldoi":"https://doi.org/10.1364/OL.43.000607","doi":"10.1364/OL.43.000607","publisher":"Optica Publishing Group","day":"01","abstract":[{"lang":"eng","text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum."}],"author":[{"last_name":"Midya","full_name":"Midya, Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","first_name":"Bikashkali"},{"last_name":"Konotop","first_name":"Vladimir","full_name":"Konotop, Vladimir"}],"isi":1,"corr_author":"1","type":"journal_article","date_published":"2018-02-01T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","quality_controlled":"1","intvolume":"        43","arxiv":1,"date_updated":"2025-06-03T11:21:56Z","publication_status":"published","department":[{"_id":"MiLe"}],"publist_id":"7388","volume":43,"acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"page":"607 - 610","citation":{"chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” <i>Optics Letters</i>. Optica Publishing Group, 2018. <a href=\"https://doi.org/10.1364/OL.43.000607\">https://doi.org/10.1364/OL.43.000607</a>.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” <i>Optics Letters</i>, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:<a href=\"https://doi.org/10.1364/OL.43.000607\">10.1364/OL.43.000607</a>.","apa":"Midya, B., &#38; Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.43.000607\">https://doi.org/10.1364/OL.43.000607</a>","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. <i>Optics Letters</i>. 2018;43(3):607-610. doi:<a href=\"https://doi.org/10.1364/OL.43.000607\">10.1364/OL.43.000607</a>","ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610.","short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” <i>Optics Letters</i>, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018."},"external_id":{"isi":["000423776600066"],"arxiv":["1711.01986"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.01986"}],"issue":"3","ec_funded":1},{"corr_author":"1","isi":1,"article_number":"060601 ","author":[{"last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","first_name":"Shabir","orcid":"0000-0003-0415-1423"},{"first_name":"Matteo","full_name":"Aquilina, Matteo","last_name":"Aquilina"},{"last_name":"Xuereb","first_name":"André","full_name":"Xuereb, André"}],"abstract":[{"text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits.","lang":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","description":"News on IST Homepage","relation":"press_release"}]},"day":"07","fulldoi":"https://doi.org/10.1103/PhysRevLett.120.060601","doi":"10.1103/PhysRevLett.120.060601","publisher":"American Physical Society","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Manipulating the flow of thermal noise in quantum devices","publication":"Physical Review Letters","status":"public","_id":"436","month":"02","year":"2018","issue":"6","ec_funded":1,"citation":{"chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">https://doi.org/10.1103/PhysRevLett.120.060601</a>.","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” <i>Physical Review Letters</i>, vol. 120, no. 6. American Physical Society, 2018.","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. <i>Physical Review Letters</i>. 2018;120(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">10.1103/PhysRevLett.120.060601</a>","ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","apa":"Barzanjeh, S., Aquilina, M., &#38; Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">https://doi.org/10.1103/PhysRevLett.120.060601</a>","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” <i>Physical Review Letters</i>, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">10.1103/PhysRevLett.120.060601</a>."},"external_id":{"arxiv":["1706.09051"],"isi":["000424382100004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09051"}],"volume":120,"project":[{"call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publist_id":"7387","date_updated":"2024-10-22T09:36:24Z","publication_status":"published","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:28Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","arxiv":1,"quality_controlled":"1","intvolume":"       120","type":"journal_article","date_published":"2018-02-07T00:00:00Z"},{"publist_id":"7386","project":[{"grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"volume":48,"acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the  scientific  support units at IST Austria for excellent technical support.   ","external_id":{"isi":["000434963700016"]},"page":"1074 - 1077","citation":{"chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” <i>European Journal of Immunology</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1002/eji.201747358\">https://doi.org/10.1002/eji.201747358</a>.","apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., &#38; Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. <i>European Journal of Immunology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/eji.201747358\">https://doi.org/10.1002/eji.201747358</a>","mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” <i>European Journal of Immunology</i>, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:<a href=\"https://doi.org/10.1002/eji.201747358\">10.1002/eji.201747358</a>.","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. <i>European Journal of Immunology</i>. 2018;48(6):1074-1077. doi:<a href=\"https://doi.org/10.1002/eji.201747358\">10.1002/eji.201747358</a>","ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.","short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” <i>European Journal of Immunology</i>, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018."},"ec_funded":1,"issue":"6","date_published":"2018-02-13T00:00:00Z","has_accepted_license":"1","type":"journal_article","intvolume":"        48","quality_controlled":"1","oa_version":"Published Version","date_created":"2018-12-11T11:46:28Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pubrep_id":"1067","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:27Z","checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb","relation":"main_file","file_id":"5044","file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:13:56Z","creator":"system","file_size":590106,"access_level":"open_access"}],"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"}],"date_updated":"2025-04-14T07:42:07Z","abstract":[{"lang":"eng","text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity."}],"author":[{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"last_name":"Haecker","first_name":"Hans","full_name":"Haecker, Hans"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"isi":1,"corr_author":"1","acknowledged_ssus":[{"_id":"SSU"}],"year":"2018","month":"02","_id":"437","status":"public","publication":"European Journal of Immunology","title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","scopus_import":"1","oa":1,"article_processing_charge":"Yes (via OA deal)","publisher":"Wiley-Blackwell","file_date_updated":"2020-07-14T12:46:27Z","doi":"10.1002/eji.201747358","ddc":["570"],"fulldoi":"https://doi.org/10.1002/eji.201747358","license":"https://creativecommons.org/licenses/by-nc/4.0/","day":"13"},{"type":"journal_article","has_accepted_license":"1","date_published":"2018-04-06T00:00:00Z","pubrep_id":"971","language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:29Z","intvolume":"        46","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_updated":"2020-07-14T12:46:27Z","file_id":"5151","relation":"main_file","checksum":"3ff4f545c27e11a4cd20ccb30778793e","content_type":"application/pdf","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","date_created":"2018-12-12T10:15:30Z","file_size":5027978,"creator":"system","access_level":"open_access"}],"date_updated":"2025-04-15T06:28:24Z","department":[{"_id":"CaGu"}],"publication_status":"published","volume":46,"project":[{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"citation":{"chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” <i>Nucleic Acids Research</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/nar/gky079\">https://doi.org/10.1093/nar/gky079</a>.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. <i>Nucleic Acids Research</i>. 2018;46(6):2918-2931. doi:<a href=\"https://doi.org/10.1093/nar/gky079\">10.1093/nar/gky079</a>","ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931.","mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” <i>Nucleic Acids Research</i>, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:<a href=\"https://doi.org/10.1093/nar/gky079\">10.1093/nar/gky079</a>.","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &#38; Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gky079\">https://doi.org/10.1093/nar/gky079</a>","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” <i>Nucleic Acids Research</i>, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018.","short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931."},"page":"2918-2931","external_id":{"isi":["000429009500021"]},"issue":"6","publication":"Nucleic Acids Research","_id":"438","status":"public","month":"04","year":"2018","article_processing_charge":"Yes (in subscription journal)","oa":1,"scopus_import":"1","title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","fulldoi":"https://doi.org/10.1093/nar/gky079","ddc":["576"],"file_date_updated":"2020-07-14T12:46:27Z","doi":"10.1093/nar/gky079","publisher":"Oxford University Press","day":"06","abstract":[{"lang":"eng","text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress."}],"related_material":{"record":[{"status":"public","id":"5569","relation":"popular_science"}]},"author":[{"last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias"},{"full_name":"Vandervelde, Alexandra","first_name":"Alexandra","last_name":"Vandervelde"},{"last_name":"Albanese","full_name":"Albanese, Tanino","first_name":"Tanino"},{"last_name":"Gelens","first_name":"Lendert","full_name":"Gelens, Lendert"},{"full_name":"Moll, Isabella","first_name":"Isabella","last_name":"Moll"}],"corr_author":"1","isi":1},{"acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"article_number":"155134","author":[{"first_name":"C J","full_name":"Turner, C J","last_name":"Turner"},{"orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios","last_name":"Michailidis"},{"last_name":"Abanin","first_name":"D A","full_name":"Abanin, D A"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827"},{"last_name":"Papić","full_name":"Papić, Z","first_name":"Z"}],"abstract":[{"text":"Recent realization of a kinetically constrained chain of Rydberg atoms by Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation of unusual revivals in the many-body quantum dynamics. In our previous work [C. J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to the existence of “quantum scarred” eigenstates in the many-body spectrum of the experimentally realized model. Here, we present a detailed study of the eigenstate properties of the same model. We find that the majority of the eigenstates exhibit anomalous thermalization: the observable expectation values converge to their Gibbs ensemble values, but parametrically slower compared to the predictions of the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum, we identify nonergodic eigenstates that strongly violate the ETH, whose number grows polynomially with system size. Previously, the same eigenstates were identified via large overlaps with certain product states, and were used to explain the revivals observed in experiment. Here, we find that these eigenstates, in addition to highly atypical expectation values of local observables, also exhibit subthermal entanglement entropy that scales logarithmically with the system size. Moreover, we identify an additional class of quantum scarred eigenstates, and discuss their manifestations in the dynamics starting from initial product states. We use forward scattering approximation to describe the structure and physical properties of quantum scarred eigenstates. Finally, we discuss the stability of quantum scars to various perturbations. We observe that quantum scars remain robust when the introduced perturbation is compatible with the forward scattering approximation. In contrast, the perturbations which most efficiently destroy quantum scars also lead to the restoration of “canonical” thermalization.","lang":"eng"}],"day":"22","fulldoi":"https://doi.org/10.1103/PhysRevB.98.155134","doi":"10.1103/PhysRevB.98.155134","publisher":"American Physical Society","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations","publication":"Physical Review B","_id":"44","month":"10","status":"public","year":"2018","issue":"15","citation":{"ista":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 98(15), 155134.","ama":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. 2018;98(15). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>","mla":"Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>.","apa":"Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., &#38; Papić, Z. (2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>","ieee":"C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations,” <i>Physical Review B</i>, vol. 98, no. 15. American Physical Society, 2018.","short":"C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review B 98 (2018).","chicago":"Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>."},"external_id":{"arxiv":["1806.10933"],"isi":["000447919100001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10933"}],"volume":98,"publist_id":"8010","date_updated":"2023-10-10T13:28:49Z","publication_status":"published","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","intvolume":"        98","quality_controlled":"1","arxiv":1,"type":"journal_article","date_published":"2018-10-22T00:00:00Z"},{"isi":1,"author":[{"last_name":"Frank","first_name":"Rupert","full_name":"Frank, Rupert"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan Thanh, Nam","first_name":"Nam","last_name":"Phan Thanh"},{"last_name":"Van Den Bosch","first_name":"Hanne","full_name":"Van Den Bosch, Hanne"}],"abstract":[{"text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z &gt; 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential.","lang":"eng"}],"day":"01","fulldoi":"https://doi.org/10.1002/cpa.21717","publisher":"Wiley-Blackwell","doi":"10.1002/cpa.21717","oa":1,"article_processing_charge":"No","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","publication":"Communications on Pure and Applied Mathematics","year":"2018","status":"public","_id":"446","month":"03","issue":"3","external_id":{"isi":["000422675800004"],"arxiv":["1606.07355"]},"citation":{"ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” <i>Communications on Pure and Applied Mathematics</i>, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. <i>Communications on Pure and Applied Mathematics</i>. 2018;71(3):577-614. doi:<a href=\"https://doi.org/10.1002/cpa.21717\">10.1002/cpa.21717</a>","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” <i>Communications on Pure and Applied Mathematics</i>, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:<a href=\"https://doi.org/10.1002/cpa.21717\">10.1002/cpa.21717</a>.","apa":"Frank, R., Nam, P., &#38; Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cpa.21717\">https://doi.org/10.1002/cpa.21717</a>","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1002/cpa.21717\">https://doi.org/10.1002/cpa.21717</a>."},"page":"577 - 614","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07355"}],"acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","volume":71,"publist_id":"7377","date_updated":"2023-09-19T10:09:40Z","publication_status":"published","department":[{"_id":"RoSe"}],"article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","date_created":"2018-12-11T11:46:31Z","language":[{"iso":"eng"}],"intvolume":"        71","arxiv":1,"quality_controlled":"1","type":"journal_article","date_published":"2018-03-01T00:00:00Z"},{"isi":1,"abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"related_material":{"record":[{"id":"9841","relation":"research_data","status":"public"}]},"author":[{"full_name":"Harrison, Mark","first_name":"Mark","last_name":"Harrison"},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"last_name":"Robertson","full_name":"Robertson, Hugh","first_name":"Hugh"},{"first_name":"Nicolas","full_name":"Arning, Nicolas","last_name":"Arning"},{"last_name":"Bitard Feildel","full_name":"Bitard Feildel, Tristan","first_name":"Tristan"},{"last_name":"Chao","full_name":"Chao, Hsu","first_name":"Hsu"},{"first_name":"Christopher","full_name":"Childers, Christopher","last_name":"Childers"},{"last_name":"Dinh","first_name":"Huyen","full_name":"Dinh, Huyen"},{"last_name":"Doddapaneni","first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan"},{"last_name":"Dugan","first_name":"Shannon","full_name":"Dugan, Shannon"},{"first_name":"Johannes","full_name":"Gowin, Johannes","last_name":"Gowin"},{"last_name":"Greiner","first_name":"Carolin","full_name":"Greiner, Carolin"},{"first_name":"Yi","full_name":"Han, Yi","last_name":"Han"},{"full_name":"Hu, Haofu","first_name":"Haofu","last_name":"Hu"},{"last_name":"Hughes","first_name":"Daniel","full_name":"Hughes, Daniel"},{"last_name":"Huylmans","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"last_name":"Kemena","first_name":"Karsten","full_name":"Kemena, Karsten"},{"first_name":"Lukas","full_name":"Kremer, Lukas","last_name":"Kremer"},{"first_name":"Sandra","full_name":"Lee, Sandra","last_name":"Lee"},{"full_name":"López Ezquerra, Alberto","first_name":"Alberto","last_name":"López Ezquerra"},{"last_name":"Mallet","first_name":"Ludovic","full_name":"Mallet, Ludovic"},{"first_name":"Jose","full_name":"Monroy Kuhn, Jose","last_name":"Monroy Kuhn"},{"first_name":"Annabell","full_name":"Moser, Annabell","last_name":"Moser"},{"full_name":"Murali, Shwetha","first_name":"Shwetha","last_name":"Murali"},{"last_name":"Muzny","first_name":"Donna","full_name":"Muzny, Donna"},{"first_name":"Saria","full_name":"Otani, Saria","last_name":"Otani"},{"last_name":"Piulachs","first_name":"Maria","full_name":"Piulachs, Maria"},{"first_name":"Monica","full_name":"Poelchau, Monica","last_name":"Poelchau"},{"last_name":"Qu","first_name":"Jiaxin","full_name":"Qu, Jiaxin"},{"last_name":"Schaub","first_name":"Florentine","full_name":"Schaub, Florentine"},{"last_name":"Wada Katsumata","first_name":"Ayako","full_name":"Wada Katsumata, Ayako"},{"full_name":"Worley, Kim","first_name":"Kim","last_name":"Worley"},{"last_name":"Xie","full_name":"Xie, Qiaolin","first_name":"Qiaolin"},{"first_name":"Guillem","full_name":"Ylla, Guillem","last_name":"Ylla"},{"last_name":"Poulsen","full_name":"Poulsen, Michael","first_name":"Michael"},{"last_name":"Gibbs","first_name":"Richard","full_name":"Gibbs, Richard"},{"last_name":"Schal","full_name":"Schal, Coby","first_name":"Coby"},{"last_name":"Richards","full_name":"Richards, Stephen","first_name":"Stephen"},{"full_name":"Belles, Xavier","first_name":"Xavier","last_name":"Belles"},{"last_name":"Korb","full_name":"Korb, Judith","first_name":"Judith"},{"last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich","first_name":"Erich"}],"fulldoi":"https://doi.org/10.1038/s41559-017-0459-1","ddc":["576"],"file_date_updated":"2020-07-14T12:46:30Z","doi":"10.1038/s41559-017-0459-1","publisher":"Springer Nature","day":"05","publication":"Nature Ecology and Evolution","_id":"448","status":"public","month":"02","year":"2018","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","citation":{"chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>.","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. 2018;2(3):557-566. doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>","ieee":"M. Harrison <i>et al.</i>, “Hemimetabolous genomes reveal molecular basis of termite eusociality,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566."},"page":"557-566","external_id":{"isi":["000426559600026"]},"issue":"3","publist_id":"7375","volume":2,"acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:30Z","relation":"main_file","checksum":"874953136ac125e65f37971d3cabc5b7","file_id":"4731","access_level":"open_access","date_created":"2018-12-12T10:09:08Z","creator":"system","file_size":3730583}],"date_updated":"2023-09-11T14:10:57Z","publication_status":"published","department":[{"_id":"BeVi"}],"type":"journal_article","has_accepted_license":"1","date_published":"2018-02-05T00:00:00Z","pubrep_id":"969","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:32Z","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","intvolume":"         2"},{"publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:46:31Z","doi":"10.1038/s41467-017-02721-8","fulldoi":"https://doi.org/10.1038/s41467-017-02721-8","ddc":["004"],"day":"07","year":"2018","_id":"454","month":"02","status":"public","publication":"Nature Communications","title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","scopus_import":"1","oa":1,"article_processing_charge":"No","article_number":"555","isi":1,"abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games."}],"author":[{"last_name":"Reiter","orcid":"0000-0002-0170-7353","first_name":"Johannes","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"first_name":"David","full_name":"Rand, David","last_name":"Rand"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"file":[{"creator":"system","file_size":843646,"date_created":"2018-12-12T10:09:18Z","access_level":"open_access","checksum":"b6b90367545b4c615891c960ab0567f1","relation":"main_file","file_id":"4741","date_updated":"2020-07-14T12:46:31Z","file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","department":[{"_id":"KrCh"}],"date_updated":"2025-04-15T06:30:05Z","date_published":"2018-02-07T00:00:00Z","has_accepted_license":"1","type":"journal_article","quality_controlled":"1","intvolume":"         9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:34Z","oa_version":"Published Version","language":[{"iso":"eng"}],"pubrep_id":"964","external_id":{"isi":["000424318200001"]},"citation":{"ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-02721-8\">10.1038/s41467-017-02721-8</a>","ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555.","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” <i>Nature Communications</i>, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-017-02721-8\">10.1038/s41467-017-02721-8</a>.","apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., &#38; Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-02721-8\">https://doi.org/10.1038/s41467-017-02721-8</a>","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-017-02721-8\">https://doi.org/10.1038/s41467-017-02721-8</a>."},"ec_funded":1,"issue":"1","publist_id":"7368","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"volume":9,"acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson."},{"alternative_title":["Annales Henri Poincare"],"publication":"Annales Henri Poincare","year":"2018","month":"04","_id":"455","status":"public","oa":1,"article_processing_charge":"No","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","scopus_import":"1","ddc":["510","539"],"fulldoi":"https://doi.org/10.1007/s00023-018-0644-z","publisher":"Birkhäuser","file_date_updated":"2020-07-14T12:46:31Z","doi":"10.1007/s00023-018-0644-z","day":"01","abstract":[{"lang":"eng","text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities"}],"author":[{"last_name":"Benedikter","orcid":"0000-0002-1071-6091","first_name":"Niels P","full_name":"Benedikter, Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sok, Jérémy","first_name":"Jérémy","last_name":"Sok"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"corr_author":"1","isi":1,"has_accepted_license":"1","type":"journal_article","date_published":"2018-04-01T00:00:00Z","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:34Z","language":[{"iso":"eng"}],"pubrep_id":"993","intvolume":"        19","quality_controlled":"1","file":[{"file_id":"4914","checksum":"883eeccba8384ad7fcaa28761d99a0fa","relation":"main_file","date_updated":"2020-07-14T12:46:31Z","content_type":"application/pdf","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","file_size":923252,"creator":"system","date_created":"2018-12-12T10:11:57Z","access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2024-10-09T20:58:43Z","department":[{"_id":"RoSe"}],"publication_status":"published","publist_id":"7367","volume":19,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","external_id":{"isi":["000427578900006"]},"citation":{"chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” <i>Annales Henri Poincare</i>. Birkhäuser, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0644-z\">https://doi.org/10.1007/s00023-018-0644-z</a>.","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. <i>Annales Henri Poincare</i>. 2018;19(4):1167-1214. doi:<a href=\"https://doi.org/10.1007/s00023-018-0644-z\">10.1007/s00023-018-0644-z</a>","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” <i>Annales Henri Poincare</i>, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:<a href=\"https://doi.org/10.1007/s00023-018-0644-z\">10.1007/s00023-018-0644-z</a>.","apa":"Benedikter, N. P., Sok, J., &#38; Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. <i>Annales Henri Poincare</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00023-018-0644-z\">https://doi.org/10.1007/s00023-018-0644-z</a>","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” <i>Annales Henri Poincare</i>, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214."},"page":"1167 - 1214","issue":"4"},{"article_number":"eaar7514","corr_author":"1","citation":{"ista":"Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514.","ama":"Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. <i>Science Translational Medicine</i>. 2018;10(423). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aar7514\">10.1126/scitranslmed.aar7514</a>","apa":"Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aar7514\">https://doi.org/10.1126/scitranslmed.aar7514</a>","mla":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” <i>Science Translational Medicine</i>, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aar7514\">10.1126/scitranslmed.aar7514</a>.","ieee":"G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” <i>Science Translational Medicine</i>, vol. 10, no. 423. American Association for the Advancement of Science, 2018.","short":"G. Novarino, Science Translational Medicine 10 (2018).","chicago":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2018. <a href=\"https://doi.org/10.1126/scitranslmed.aar7514\">https://doi.org/10.1126/scitranslmed.aar7514</a>."},"issue":"423","publist_id":"7365","abstract":[{"text":"Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. ","lang":"eng"}],"author":[{"orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino"}],"volume":10,"publisher":"American Association for the Advancement of Science","doi":"10.1126/scitranslmed.aar7514","fulldoi":"https://doi.org/10.1126/scitranslmed.aar7514","publication_status":"published","day":"10","department":[{"_id":"GaNo"}],"date_updated":"2024-10-09T20:58:46Z","year":"2018","_id":"456","date_published":"2018-01-10T00:00:00Z","month":"01","status":"public","type":"journal_article","publication":"Science Translational Medicine","title":"Zika-associated microcephaly: Reduce the stress and race for the treatment","quality_controlled":"1","intvolume":"        10","scopus_import":1,"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:34Z","language":[{"iso":"eng"}]},{"publication":"Nature Ecology and Evolution","year":"2018","month":"02","_id":"457","status":"public","article_processing_charge":"No","title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41559-017-0424-z","publisher":"Springer Nature","doi":"10.1038/s41559-017-0424-z","day":"01","abstract":[{"text":"Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"202"}]},"author":[{"last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","first_name":"Maros","orcid":"0000-0001-7460-7479"},{"first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","last_name":"Lang"},{"first_name":"Dominik","full_name":"Refardt, Dominik","last_name":"Refardt"},{"last_name":"Levin","first_name":"Bruce","full_name":"Levin, Bruce"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"isi":1,"corr_author":"1","type":"journal_article","date_published":"2018-02-01T00:00:00Z","oa_version":"None","date_created":"2018-12-11T11:46:35Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"         2","date_updated":"2026-04-08T14:19:43Z","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publist_id":"7364","volume":2,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level"}],"external_id":{"isi":["000426516400027"]},"citation":{"ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. <i>Nature Ecology and Evolution</i>. 2018;2(2):359-366. doi:<a href=\"https://doi.org/10.1038/s41559-017-0424-z\">10.1038/s41559-017-0424-z</a>","ista":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366.","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., &#38; Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0424-z\">https://doi.org/10.1038/s41559-017-0424-z</a>","mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:<a href=\"https://doi.org/10.1038/s41559-017-0424-z\">10.1038/s41559-017-0424-z</a>.","ieee":"M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.","chicago":"Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41559-017-0424-z\">https://doi.org/10.1038/s41559-017-0424-z</a>."},"page":"359 - 366","issue":"2","ec_funded":1},{"date_published":"2018-04-01T00:00:00Z","type":"journal_article","arxiv":1,"quality_controlled":"1","intvolume":"       370","date_created":"2018-12-11T11:46:35Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publication_status":"published","date_updated":"2025-06-04T08:06:10Z","publist_id":"7363","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]","volume":370,"main_file_link":[{"url":"https://arxiv.org/abs/1602.04637","open_access":"1"}],"external_id":{"isi":["000423197800019"],"arxiv":["1602.04637"]},"page":"2825 - 2854","citation":{"chicago":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2018. <a href=\"https://doi.org/10.1090/tran/7292\">https://doi.org/10.1090/tran/7292</a>.","ista":"Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854.","ama":"Akopyan A, Bobenko A. Incircular nets and confocal conics. <i>Transactions of the American Mathematical Society</i>. 2018;370(4):2825-2854. doi:<a href=\"https://doi.org/10.1090/tran/7292\">10.1090/tran/7292</a>","apa":"Akopyan, A., &#38; Bobenko, A. (2018). Incircular nets and confocal conics. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/7292\">https://doi.org/10.1090/tran/7292</a>","mla":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” <i>Transactions of the American Mathematical Society</i>, vol. 370, no. 4, American Mathematical Society, 2018, pp. 2825–54, doi:<a href=\"https://doi.org/10.1090/tran/7292\">10.1090/tran/7292</a>.","ieee":"A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” <i>Transactions of the American Mathematical Society</i>, vol. 370, no. 4. American Mathematical Society, pp. 2825–2854, 2018.","short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854."},"ec_funded":1,"issue":"4","year":"2018","month":"04","_id":"458","status":"public","publication":"Transactions of the American Mathematical Society","title":"Incircular nets and confocal conics","scopus_import":"1","oa":1,"article_processing_charge":"No","publisher":"American Mathematical Society","doi":"10.1090/tran/7292","fulldoi":"https://doi.org/10.1090/tran/7292","day":"01","abstract":[{"lang":"eng","text":"We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem."}],"author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"last_name":"Bobenko","first_name":"Alexander","full_name":"Bobenko, Alexander"}],"isi":1,"corr_author":"1"}]