[{"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10","end_date":"2018-07-15","location":"Stockholm, Sweden"},"type":"conference","status":"public","_id":"6012","department":[{"_id":"ChLa"}],"date_updated":"2023-10-17T09:50:53Z","main_file_link":[{"url":"https://arxiv.org/abs/1806.07259","open_access":"1"}],"scopus_import":"1","intvolume":" 80","month":"02","abstract":[{"text":"We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task.","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"volume":80,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"external_id":{"arxiv":["1806.07259"],"isi":["000683379204058"]},"article_processing_charge":"No","author":[{"full_name":"Sahoo, Subham","last_name":"Sahoo","first_name":"Subham"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"}],"title":"Learning equations for extrapolation and control","citation":{"mla":"Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 4442–50.","ieee":"S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation and control,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.","short":"S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450.","ama":"Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:4442-4450.","apa":"Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for extrapolation and control. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research Press.","chicago":"Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations for Extrapolation and Control.” In Proceedings of the 35th International Conference on Machine Learning, 80:4442–50. ML Research Press, 2018.","ista":"Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation and control. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 4442–4450."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"ML Research Press","quality_controlled":"1","page":"4442-4450","date_created":"2019-02-14T15:21:07Z","date_published":"2018-02-01T00:00:00Z","year":"2018","isi":1,"publication":"Proceedings of the 35th International Conference on Machine Learning","day":"01"},{"oa":1,"publisher":"ML Research Press","quality_controlled":"1","page":"2815-2824","date_created":"2019-02-14T14:51:57Z","date_published":"2018-02-01T00:00:00Z","year":"2018","isi":1,"publication":"Proceedings of the 35 th International Conference on Machine Learning","day":"01","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"external_id":{"isi":["000683379202095"],"arxiv":["1703.01678"]},"article_processing_charge":"No","author":[{"first_name":"Ilja","full_name":"Kuzborskij, Ilja","last_name":"Kuzborskij"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"title":"Data-dependent stability of stochastic gradient descent","citation":{"chicago":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” In Proceedings of the 35 Th International Conference on Machine Learning, 80:2815–24. ML Research Press, 2018.","ista":"Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient descent. Proceedings of the 35 th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 2815–2824.","mla":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” Proceedings of the 35 Th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.","ieee":"I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient descent,” in Proceedings of the 35 th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","apa":"Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic gradient descent. In Proceedings of the 35 th International Conference on Machine Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.","ama":"Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent. In: Proceedings of the 35 Th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:2815-2824."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01678"}],"scopus_import":"1","intvolume":" 80","month":"02","abstract":[{"lang":"eng","text":"We establish a data-dependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distribution-free algorithmic stability results for SGD which depend on the worst-case constants. By virtue of the data-dependent argument, our bounds provide new insights into learning with SGD on convex and non-convex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the non-convex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. "}],"oa_version":"Preprint","ec_funded":1,"volume":80,"publication_status":"published","language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10","location":"Stockholm, Sweden","end_date":"2018-07-15"},"type":"conference","status":"public","_id":"6011","department":[{"_id":"ChLa"}],"date_updated":"2023-10-17T09:51:13Z"},{"department":[{"_id":"DaAl"},{"_id":"ChLa"}],"date_updated":"2023-10-17T11:47:20Z","type":"conference","conference":{"start_date":"2018-12-02","location":"Montreal, Canada","end_date":"2018-12-08","name":"NeurIPS: Conference on Neural Information Processing Systems"},"status":"public","_id":"6589","volume":"Volume 2018","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.10505"}],"month":"12","abstract":[{"text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics.","lang":"eng"}],"oa_version":"Preprint","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Hoefler","full_name":"Hoefler, Torsten","first_name":"Torsten"},{"last_name":"Johansson","full_name":"Johansson, Mikael","first_name":"Mikael"},{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sarit","full_name":"Khirirat, Sarit","last_name":"Khirirat"},{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"}],"article_processing_charge":"No","external_id":{"isi":["000461852000047"],"arxiv":["1809.10505"]},"title":"The convergence of sparsified gradient methods","citation":{"mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” Advances in Neural Information Processing Systems 31, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83.","ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: Advances in Neural Information Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., & Renggli, C. (2018). The convergence of sparsified gradient methods. In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.","short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in Advances in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018.","ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"5973-5983","date_published":"2018-12-01T00:00:00Z","date_created":"2019-06-27T09:32:55Z","isi":1,"year":"2018","day":"01","publication":"Advances in Neural Information Processing Systems 31","quality_controlled":"1","publisher":"Neural Information Processing Systems Foundation","oa":1},{"project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"}],"title":"Social network plasticity decreases disease transmission in a eusocial insect","article_processing_charge":"No","external_id":{"isi":["000451124500041"]},"author":[{"first_name":"Nathalie","last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Crespi","full_name":"Crespi, Alessandro","first_name":"Alessandro"},{"first_name":"Danielle","full_name":"Mersch, Danielle","last_name":"Mersch"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"last_name":"Keller","full_name":"Keller, Laurent","first_name":"Laurent"}],"publist_id":"8049","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. Science. 2018;362(6417):941-945. doi:10.1126/science.aat4793","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Science. AAAS. https://doi.org/10.1126/science.aat4793","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect,” Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science 362 (2018) 941–945.","mla":"Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45, doi:10.1126/science.aat4793.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect. Science. 362(6417), 941–945.","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793."},"oa":1,"quality_controlled":"1","publisher":"AAAS","acknowledgement":"This project was funded by two European Research Council Advanced Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research Council Starting Grant (SocialVaccines, 243071) to S.C.","date_created":"2018-12-11T11:44:07Z","doi":"10.1126/science.aat4793","date_published":"2018-11-23T00:00:00Z","page":"941 - 945","publication":"Science","day":"23","year":"2018","isi":1,"status":"public","type":"journal_article","article_type":"original","_id":"7","department":[{"_id":"SyCr"}],"date_updated":"2023-10-17T11:50:05Z","intvolume":" 362","month":"11","main_file_link":[{"open_access":"1","url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups.","lang":"eng"}],"ec_funded":1,"issue":"6417","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/","relation":"press_release"}],"record":[{"id":"13055","status":"public","relation":"research_data"}]},"volume":362,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1095-9203"]}},{"intvolume":" 35","month":"08","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","pmid":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."}],"volume":35,"issue":"11","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0737-4038"]},"status":"public","article_type":"original","type":"journal_article","_id":"19","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_updated":"2023-10-17T11:51:06Z","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","date_created":"2018-12-11T11:44:11Z","date_published":"2018-08-28T00:00:00Z","doi":"10.1093/molbev/msy163","page":"2669 - 2684","publication":"Molecular Biology and Evolution","day":"28","year":"2018","isi":1,"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","article_processing_charge":"No","external_id":{"isi":["000452567200006"],"pmid":["30169679"]},"author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"last_name":"Chait","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"publist_id":"8036","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy163","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.","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.","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163."}},{"day":"08","publication":"Journal of visualized experiments","language":[{"iso":"eng"}],"isi":1,"year":"2018","publication_status":"published","volume":141,"doi":"10.3791/58585","date_published":"2018-11-08T00:00:00Z","date_created":"2018-12-11T11:44:07Z","oa_version":"None","abstract":[{"lang":"eng","text":"Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies."}],"month":"11","intvolume":" 141","quality_controlled":"1","publisher":"MyJove Corporation","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments, vol. 141, MyJove Corporation, 2018, doi:10.3791/58585.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal of Visualized Experiments 141 (2018).","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for characterising lesions and locating electrodes in small animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation, 2018.","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 2018;141. doi:10.3791/58585","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of Visualized Experiments. MyJove Corporation. https://doi.org/10.3791/58585","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments. MyJove Corporation, 2018. https://doi.org/10.3791/58585.","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 141."},"date_updated":"2023-10-17T11:49:25Z","department":[{"_id":"MaJö"}],"title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","publist_id":"8050","author":[{"first_name":"Javier","last_name":"Masís","full_name":"Masís, Javier"},{"first_name":"David","last_name":"Mankus","full_name":"Mankus, David"},{"full_name":"Wolff, Steffen","last_name":"Wolff","first_name":"Steffen"},{"first_name":"Grigori","last_name":"Guitchounts","full_name":"Guitchounts, Grigori"},{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"},{"first_name":"David","full_name":"Cox, David","last_name":"Cox"}],"external_id":{"isi":["000456469400103"]},"article_processing_charge":"No","_id":"6","status":"public","type":"journal_article"},{"article_processing_charge":"No","author":[{"last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"full_name":"Crespi, Alessandro","last_name":"Crespi","first_name":"Alessandro"},{"first_name":"Danielle","full_name":"Mersch, Danielle","last_name":"Mersch"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Keller","full_name":"Keller, Laurent"}],"title":"Social network plasticity decreases disease transmission in a eusocial insect","department":[{"_id":"SyCr"}],"citation":{"apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","mla":"Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, 10.5281/ZENODO.1322669.","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669."},"date_updated":"2023-10-17T11:50:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13055","date_created":"2023-05-23T13:24:51Z","doi":"10.5281/ZENODO.1322669","date_published":"2018-10-23T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"7","status":"public"}]},"year":"2018","day":"23","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"publisher":"Zenodo","month":"10","abstract":[{"lang":"eng","text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n - correction of URLs within README.txt file\r\n"}],"oa_version":"Published Version"},{"page":"1210 - 1219","date_created":"2018-12-11T11:44:12Z","doi":"10.1364/OPTICA.5.001210","date_published":"2018-10-20T00:00:00Z","year":"2018","isi":1,"publication":"Optica","day":"20","oa":1,"quality_controlled":"1","external_id":{"isi":["000447853100007"]},"article_processing_charge":"No","author":[{"last_name":"Botello","full_name":"Botello, Gabriel","first_name":"Gabriel"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abdalmalak, Kerlos","last_name":"Abdalmalak","first_name":"Kerlos"},{"first_name":"Elliott","last_name":"Brown","full_name":"Brown, Elliott"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Sascha","last_name":"Preu","full_name":"Preu, Sascha"},{"full_name":"Segovia Vargas, Daniel","last_name":"Segovia Vargas","first_name":"Daniel"},{"full_name":"Strekalov, Dmitry","last_name":"Strekalov","first_name":"Dmitry"},{"first_name":"Luis","last_name":"Munoz","full_name":"Munoz, Luis"},{"first_name":"Harald","full_name":"Schwefel, Harald","last_name":"Schwefel"}],"publist_id":"8033","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","citation":{"ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219.","chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, 2018. https://doi.org/10.1364/OPTICA.5.001210.","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219.","ieee":"G. Botello et al., “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” Optica, vol. 5, no. 10. pp. 1210–1219, 2018.","apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210","ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210","mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10, 2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":5,"issue":"10","publication_status":"published","publication_identifier":{"issn":["23342536"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"scopus_import":"1","intvolume":" 5","month":"10","abstract":[{"lang":"eng","text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems."}],"oa_version":"Published Version","department":[{"_id":"JoFi"}],"date_updated":"2023-10-17T12:12:40Z","type":"journal_article","article_type":"original","status":"public","_id":"22"},{"article_type":"original","type":"journal_article","status":"public","_id":"5677","department":[{"_id":"ToHe"}],"date_updated":"2023-10-17T11:53:09Z","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00757488/"}],"scopus_import":"1","intvolume":" 12","month":"05","abstract":[{"lang":"eng","text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector."}],"oa_version":"Submitted Version","issue":"2-3","volume":12,"publication_status":"published","publication_identifier":{"issn":["1551-3939"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Albert","last_name":"Benveniste","full_name":"Benveniste, Albert"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"},{"first_name":"Benoît","last_name":"Caillaud","full_name":"Caillaud, Benoît"},{"last_name":"Passerone","full_name":"Passerone, Roberto","first_name":"Roberto"},{"first_name":"Jean Baptiste","last_name":"Raclet","full_name":"Raclet, Jean Baptiste"},{"first_name":"Philipp","full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier"},{"last_name":"Sangiovanni-Vincentelli","full_name":"Sangiovanni-Vincentelli, Alberto","first_name":"Alberto"},{"last_name":"Damm","full_name":"Damm, Werner","first_name":"Werner"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Kim G.","full_name":"Larsen, Kim G.","last_name":"Larsen"}],"title":"Contracts for system design","citation":{"apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053","ieee":"A. Benveniste et al., “Contracts for system design,” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","mla":"Benveniste, Albert, et al. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:10.1561/1000000053.","ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Now Publishers","quality_controlled":"1","page":"124-400","date_created":"2018-12-16T22:59:19Z","date_published":"2018-05-01T00:00:00Z","doi":"10.1561/1000000053","year":"2018","publication":"Foundations and Trends in Electronic Design Automation","day":"01"},{"page":"607 - 610","date_created":"2018-12-11T11:46:27Z","date_published":"2018-02-01T00:00:00Z","doi":"10.1364/OL.43.000607","year":"2018","isi":1,"publication":"Optics Letters","day":"01","oa":1,"quality_controlled":"1","publisher":"Optica Publishing Group","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.","external_id":{"arxiv":["1711.01986"],"isi":["000423776600066"]},"article_processing_charge":"No","author":[{"first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali","last_name":"Midya"},{"first_name":"Vladimir","last_name":"Konotop","full_name":"Konotop, Vladimir"}],"publist_id":"7388","title":"Coherent-perfect-absorber and laser for bound states in a continuum","citation":{"ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing Group, 2018. https://doi.org/10.1364/OL.43.000607.","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607","apa":"Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.43.000607","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,” Optics Letters, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"ec_funded":1,"issue":"3","volume":43,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1711.01986","open_access":"1"}],"scopus_import":"1","intvolume":" 43","month":"02","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"MiLe"}],"date_updated":"2023-10-17T12:15:06Z","type":"journal_article","status":"public","_id":"435"},{"article_number":"30083438","author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"first_name":"Pierre","last_name":"Gagnaire","full_name":"Gagnaire, Pierre"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"first_name":"Nicolas","last_name":"Faivre","full_name":"Faivre, Nicolas"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"publist_id":"7784","external_id":{"isi":["000440484800002"]},"article_processing_charge":"No","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","citation":{"chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"PeerJ","quality_controlled":"1","oa":1,"date_published":"2018-07-30T00:00:00Z","doi":"10.7717/peerj.5198","date_created":"2018-12-11T11:44:50Z","isi":1,"has_accepted_license":"1","year":"2018","day":"30","publication":"PeerJ","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"139","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:48Z","date_updated":"2023-10-17T12:25:28Z","ddc":["576"],"scopus_import":"1","month":"07","intvolume":" 2018","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"oa_version":"Published Version","issue":"7","volume":2018,"publication_status":"published","file":[{"file_size":1480792,"date_updated":"2020-07-14T12:44:48Z","creator":"dernst","file_name":"2018_PeerJ_Fraisse.pdf","date_created":"2018-12-18T09:42:11Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7d55ae22598a1c70759cd671600cff53","file_id":"5739"}],"language":[{"iso":"eng"}]},{"volume":2018,"issue":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"2018_PeerJ_Bertl.pdf","date_created":"2018-12-17T10:46:06Z","file_size":1328344,"date_updated":"2020-07-14T12:46:06Z","creator":"dernst","checksum":"3334886c4b39678db4c4b74299ca14ba","file_id":"5692","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":"1","intvolume":" 2018","month":"10","abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"NiBa"}],"date_updated":"2023-10-17T12:24:43Z","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"33","date_created":"2018-12-11T11:44:16Z","doi":"10.7717/peerj.5325","date_published":"2018-10-01T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"PeerJ","day":"01","oa":1,"publisher":"PeerJ","quality_controlled":"1","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"article_processing_charge":"No","publist_id":"8022","author":[{"first_name":"Johanna","last_name":"Bertl","full_name":"Bertl, Johanna"},{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","last_name":"Ringbauer"},{"full_name":"Blum, Michaël","last_name":"Blum","first_name":"Michaël"}],"title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","citation":{"ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325.","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e5325"},{"_id":"5673","status":"public","type":"journal_article","date_updated":"2023-10-17T12:19:28Z","department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment."}],"month":"12","intvolume":" 4","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2055-0278"]},"publication_status":"published","issue":"12","volume":4,"ec_funded":1,"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3."},"title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","author":[{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Nature Research","oa":1,"day":"03","publication":"Nature Plants","isi":1,"year":"2018","date_published":"2018-12-03T00:00:00Z","doi":"10.1038/s41477-018-0318-3","date_created":"2018-12-16T22:59:18Z","page":"1082-1088"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073.","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:10.1098/rsif.2018.0073.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” Journal of the Royal Society Interface, vol. 15, no. 140. The Royal Society, 2018.","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. Journal of the Royal Society Interface. 2018;15(140). doi:10.1098/rsif.2018.0073","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language acquisition with communication between learners. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073"},"title":"Language acquisition with communication between learners","article_processing_charge":"No","external_id":{"pmid":["29593089"],"isi":["000428576200023"]},"author":[{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"publist_id":"7715","article_number":"20180073","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication":"Journal of the Royal Society Interface","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:45:09Z","doi":"10.1098/rsif.2018.0073","date_published":"2018-03-01T00:00:00Z","oa":1,"publisher":"The Royal Society","quality_controlled":"1","ddc":["000"],"date_updated":"2023-10-18T06:36:00Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:22Z","_id":"198","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"file_id":"5955","checksum":"444e1a9d98eb0e780671be82b13025f3","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-02-12T07:54:37Z","file_name":"2018_RS_IbsenJensen.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_size":219837}],"publication_status":"published","publication_identifier":{"eissn":["1742-5662"]},"ec_funded":1,"volume":15,"issue":"140","related_material":{"record":[{"id":"9814","status":"public","relation":"research_data"}],"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971","relation":"supplementary_material"}]},"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students."}],"intvolume":" 15","month":"03","scopus_import":"1"},{"has_accepted_license":"1","isi":1,"year":"2018","day":"12","publication":"Royal Society Open Science","doi":"10.1098/rsos.181286","date_published":"2018-12-12T00:00:00Z","date_created":"2019-01-20T22:59:18Z","acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","publisher":"The Royal Society","quality_controlled":"1","oa":1,"citation":{"ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra"},{"first_name":"Martí Sànchez","last_name":"Fibla","full_name":"Fibla, Martí Sànchez"},{"last_name":"Valverde","full_name":"Valverde, Sergi","first_name":"Sergi"},{"first_name":"Ricard","full_name":"Solé, Ricard","last_name":"Solé"}],"external_id":{"isi":["000456566500027"],"pmid":["30662738"]},"article_processing_charge":"No","title":"Chromatic transitions in the emergence of syntax networks","article_number":"181286","publication_identifier":{"issn":["2054-5703"]},"publication_status":"published","file":[{"file_name":"2018_RoyalSocOS_Corominas.pdf","date_created":"2019-02-05T14:38:09Z","file_size":646732,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","checksum":"9664d4417f6b792242e31eea77ce9501","file_id":"5924","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":5,"issue":"12","abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"12","intvolume":" 5","date_updated":"2023-10-18T06:41:12Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"_id":"5859","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"author":[{"last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.07752"]},"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","department":[{"_id":"LaEr"}],"date_updated":"2023-12-18T10:46:08Z","citation":{"ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. .","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","status":"public","_id":"6183","article_number":"1804.07752","related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"},{"relation":"later_version","id":"14694","status":"public"}]},"date_published":"2018-04-20T00:00:00Z","date_created":"2019-03-28T09:20:06Z","publication_status":"submitted","year":"2018","day":"20","language":[{"iso":"eng"}],"publication":"arXiv","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.07752","open_access":"1"}],"month":"04","abstract":[{"lang":"eng","text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases."}],"oa_version":"Preprint"},{"doi":"10.48550/arXiv.1804.03057","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8156"}]},"date_published":"2018-09-13T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:44:30Z","day":"13","language":[{"iso":"eng"}],"publication_status":"published","year":"2018","month":"09","publisher":"arXiv","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.03057","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higher-dimensional generalization.","lang":"eng"}],"title":"Convex fair partitions into arbitrary number of pieces","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"first_name":"Roman","full_name":"Karasev, Roman","last_name":"Karasev"}],"external_id":{"arxiv":["1804.03057"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-18T10:51:02Z","citation":{"chicago":"Akopyan, Arseniy, Sergey Avvakumov, and Roman Karasev. “Convex Fair Partitions into Arbitrary Number of Pieces.” arXiv, 2018. https://doi.org/10.48550/arXiv.1804.03057.","ista":"Akopyan A, Avvakumov S, Karasev R. 2018. Convex fair partitions into arbitrary number of pieces. 1804.03057.","mla":"Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.","ama":"Akopyan A, Avvakumov S, Karasev R. Convex fair partitions into arbitrary number of pieces. 2018. doi:10.48550/arXiv.1804.03057","apa":"Akopyan, A., Avvakumov, S., & Karasev, R. (2018). Convex fair partitions into arbitrary number of pieces. arXiv. https://doi.org/10.48550/arXiv.1804.03057","ieee":"A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary number of pieces.” arXiv, 2018.","short":"A. Akopyan, S. Avvakumov, R. Karasev, (2018)."},"project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"status":"public","type":"preprint","article_number":"1804.03057","_id":"75"},{"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:03Z","ddc":["500"],"date_updated":"2024-02-20T10:48:17Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"556","ec_funded":1,"issue":"12","volume":19,"language":[{"iso":"eng"}],"file":[{"file_id":"5866","checksum":"0c38abe73569b7166b7487ad5d23cc68","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_Annales_Betea.pdf","date_created":"2019-01-21T15:18:55Z","file_size":3084674,"date_updated":"2020-07-14T12:47:03Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"intvolume":" 19","month":"11","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions."}],"title":"The free boundary Schur process and applications I","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1704.05809"]},"author":[{"last_name":"Betea","full_name":"Betea, Dan","first_name":"Dan"},{"first_name":"Jeremie","full_name":"Bouttier, Jeremie","last_name":"Bouttier"},{"first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter","last_name":"Nejjar"},{"full_name":"Vuletic, Mirjana","last_name":"Vuletic","first_name":"Mirjana"}],"publist_id":"7258","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary Schur process and applications I. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-018-0723-1","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1."},"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"date_created":"2018-12-11T11:47:09Z","date_published":"2018-11-13T00:00:00Z","doi":"10.1007/s00023-018-0723-1","page":"3663-3742","publication":"Annales Henri Poincare","day":"13","year":"2018","has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"date_updated":"2024-02-21T13:41:17Z","citation":{"short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","ieee":"H. Alhaija, A. Sellent, D. Kondermann, and C. Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018.","ama":"Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. 2018. doi:10.15479/AT:ISTA:82","apa":"Alhaija, H., Sellent, A., Kondermann, D., & Rother, C. (2018). Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:82","mla":"Alhaija, Hassan, et al. Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:82.","ista":"Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology Austria, 10.15479/AT:ISTA:82.","chicago":"Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother. “Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:82."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["001"],"article_processing_charge":"No","author":[{"first_name":"Hassan","full_name":"Alhaija, Hassan","last_name":"Alhaija"},{"first_name":"Anita","full_name":"Sellent, Anita","last_name":"Sellent"},{"first_name":"Daniel","full_name":"Kondermann, Daniel","last_name":"Kondermann"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:47:05Z","title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","_id":"5573","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","keyword":["graph matching","quadratic assignment problem<"],"status":"public","datarep_id":"82","year":"2018","has_accepted_license":"1","file":[{"checksum":"53c17082848e12f3c2e1b4185b578208","file_id":"5600","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:02:34Z","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","date_updated":"2020-07-14T12:47:05Z","file_size":1737958,"creator":"system"}],"day":"04","contributor":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Paul","last_name":"Swoboda"}],"date_created":"2018-12-12T12:31:36Z","doi":"10.15479/AT:ISTA:82","related_material":{"link":[{"relation":"research_paper","url":"https://doi.org/10.1007/978-3-319-24947-6_23"}]},"date_published":"2018-01-04T00:00:00Z","abstract":[{"lang":"eng","text":"Graph matching problems for large displacement optical flow of RGB-D images."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"01"},{"day":"10","publication":"PLoS Computational Biology","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-05-10T00:00:00Z","doi":"10.1371/journal.pcbi.1006057","date_created":"2018-12-11T11:45:39Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.","ama":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057","apa":"Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1006057","short":"V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).","ieee":"V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.","chicago":"Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.","ista":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057."},"title":"Nonlinear decoding of a complex movie from the mammalian retina","author":[{"first_name":"Vicent","id":"421234E8-F248-11E8-B48F-1D18A9856A87","last_name":"Botella Soler","full_name":"Botella Soler, Vicent","orcid":"0000-0002-8790-1914"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000434012100002"]},"article_processing_charge":"Yes","article_number":"e1006057","project":[{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"},{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26"}],"file":[{"file_id":"5974","checksum":"3026f94d235219e15514505fdbadf34e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_Plos_Botella_Soler.pdf","date_created":"2019-02-13T11:07:15Z","creator":"dernst","file_size":3460786,"date_updated":"2020-07-14T12:45:53Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":14,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/","description":"News on IST Homepage"}],"record":[{"relation":"research_data","status":"public","id":"5584"}]},"issue":"5","ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains.","lang":"eng"}],"month":"05","intvolume":" 14","scopus_import":"1","ddc":["570"],"date_updated":"2024-02-21T13:45:25Z","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:53Z","_id":"292","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"volume":46,"related_material":{"record":[{"relation":"popular_science","id":"5569","status":"public"}]},"issue":"6","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"3ff4f545c27e11a4cd20ccb30778793e","file_id":"5151","creator":"system","file_size":5027978,"date_updated":"2020-07-14T12:46:27Z","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","date_created":"2018-12-12T10:15:30Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 46","scopus_import":"1","oa_version":"Published Version","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."}],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:27Z","ddc":["576"],"date_updated":"2024-02-21T13:44:45Z","status":"public","pubrep_id":"971","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"438","date_published":"2018-04-06T00:00:00Z","doi":"10.1093/nar/gky079","date_created":"2018-12-11T11:46:29Z","page":"2918-2931","day":"06","publication":"Nucleic Acids Research","isi":1,"has_accepted_license":"1","year":"2018","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","author":[{"first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"},{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"full_name":"Vandervelde, Alexandra","last_name":"Vandervelde","first_name":"Alexandra"},{"full_name":"Albanese, Tanino","last_name":"Albanese","first_name":"Tanino"},{"full_name":"Gelens, Lendert","last_name":"Gelens","first_name":"Lendert"},{"full_name":"Moll, Isabella","last_name":"Moll","first_name":"Isabella"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000429009500021"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.","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.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.","apa":"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. Oxford University Press. https://doi.org/10.1093/nar/gky079","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, 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."},"project":[{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}]},{"project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"article_number":"e35684","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","last_name":"Picard","full_name":"Picard, Marion A","orcid":"0000-0002-8101-2518"},{"full_name":"Cosseau, Celine","last_name":"Cosseau","first_name":"Celine"},{"first_name":"Sabrina","last_name":"Ferré","full_name":"Ferré, Sabrina"},{"last_name":"Quack","full_name":"Quack, Thomas","first_name":"Thomas"},{"first_name":"Christoph","full_name":"Grevelding, Christoph","last_name":"Grevelding"},{"full_name":"Couté, Yohann","last_name":"Couté","first_name":"Yohann"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7792","external_id":{"isi":["000441388200001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684.","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","ieee":"M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684"},"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","date_published":"2018-08-13T00:00:00Z","doi":"10.7554/eLife.35684","date_created":"2018-12-11T11:44:47Z","day":"13","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2018","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"131","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:44:43Z","ddc":["570"],"date_updated":"2024-02-21T13:45:12Z","month":"08","intvolume":" 7","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. ","lang":"eng"}],"volume":7,"related_material":{"record":[{"status":"public","id":"5586","relation":"popular_science"}]},"file":[{"file_id":"5695","checksum":"d6331d4385b1fffd6b47b45d5949d841","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T11:55:05Z","file_name":"2018_eLife_Picard.pdf","date_updated":"2020-07-14T12:44:43Z","file_size":3158125,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"_id":"5584","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"project":[{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes"}],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-02-21T13:45:26Z","citation":{"ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98.","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98."},"file_date_updated":"2020-07-14T12:47:07Z","title":"Nonlinear decoding of a complex movie from the mammalian retina","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"first_name":"Stephane","last_name":"Deny","full_name":"Deny, Stephane"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Vicente","last_name":"Botella-Soler","full_name":"Botella-Soler, Vicente"},{"full_name":"Martius, Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"oa_version":"Published Version","abstract":[{"text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. ","lang":"eng"}],"month":"03","oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"file_id":"5590","checksum":"6808748837b9afbbbabc2a356ca2b88a","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","date_created":"2018-12-12T13:02:24Z","creator":"system","file_size":1142543971,"date_updated":"2020-07-14T12:47:07Z"},{"file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","date_created":"2018-12-12T13:02:25Z","creator":"system","file_size":702336,"date_updated":"2020-07-14T12:47:07Z","checksum":"d6d6cd07743038fe3a12352983fcf9dd","file_id":"5591","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_size":432,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","date_created":"2018-12-12T13:02:26Z","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","file_id":"5592","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8"},{"date_created":"2018-12-12T13:02:26Z","file_name":"IST-2018-98-v1+4_README.txt","creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":986,"file_id":"5593","checksum":"2a83b011012e21e934b4596285b1a183","access_level":"open_access","relation":"main_file","content_type":"text/plain"}],"day":"29","year":"2018","datarep_id":"98","has_accepted_license":"1","date_created":"2018-12-12T12:31:39Z","doi":"10.15479/AT:ISTA:98","related_material":{"record":[{"relation":"used_in_publication","id":"292","status":"public"}]},"date_published":"2018-03-29T00:00:00Z"},{"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"article_processing_charge":"No","external_id":{"isi":["000441753000007"]},"title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","citation":{"mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","quality_controlled":"1","acknowledgement":"ERC, Grant/Award Number: 250152","page":"988 - 999","date_published":"2018-09-01T00:00:00Z","doi":"10.1111/1755-0998.12782","date_created":"2018-12-11T11:45:37Z","isi":1,"year":"2018","day":"01","publication":"Molecular Ecology Resources","type":"journal_article","status":"public","_id":"286","department":[{"_id":"NiBa"}],"date_updated":"2024-02-21T13:45:00Z","scopus_import":"1","month":"09","intvolume":" 18","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"oa_version":"None","related_material":{"record":[{"status":"public","id":"5583","relation":"popular_science"}]},"issue":"5","volume":18,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"07","datarep_id":"109","year":"2018","has_accepted_license":"1","day":"24","file":[{"checksum":"e60b484bd6f55c08eb66a189cb72c923","file_id":"5601","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","date_created":"2018-12-12T13:02:35Z","creator":"system","file_size":11918144,"date_updated":"2020-07-14T12:47:08Z"}],"contributor":[{"last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T12:31:40Z","related_material":{"record":[{"id":"131","status":"public","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:109","date_published":"2018-07-24T00:00:00Z","_id":"5586","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","keyword":["schistosoma","Z-chromosome","gene expression"],"status":"public","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"citation":{"mla":"Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","short":"B. Vicoso, (2018).","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109."},"date_updated":"2024-02-21T13:45:12Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"file_date_updated":"2020-07-14T12:47:08Z","department":[{"_id":"BeVi"}],"title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)"},{"month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"286"}]},"doi":"10.15479/AT:ISTA:95","date_published":"2018-02-12T00:00:00Z","contributor":[{"last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T12:31:39Z","file":[{"file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","date_created":"2018-12-12T13:02:41Z","file_size":122048,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_id":"5606","checksum":"fc6aab51439f2622ba6df8632e66fd4f","content_type":"text/csv","relation":"main_file","access_level":"open_access"},{"date_created":"2018-12-12T13:02:42Z","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":235980,"checksum":"92347586ae4f8a6eb7c04354797bf314","file_id":"5607","access_level":"open_access","relation":"main_file","content_type":"text/csv"},{"file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","date_created":"2018-12-12T13:02:43Z","file_size":311712,"date_updated":"2020-07-14T12:47:07Z","creator":"system","checksum":"3300813645a54e6c5c39f41917228354","file_id":"5608","content_type":"text/csv","relation":"main_file","access_level":"open_access"},{"creator":"system","file_size":342090,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_created":"2018-12-12T13:02:44Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5609","checksum":"e739fc473567fd8f39438b445fc46147"}],"day":"12","has_accepted_license":"1","datarep_id":"95","year":"2018","status":"public","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"5583","title":"Data and Python scripts supporting Python package FAPS","file_date_updated":"2020-07-14T12:47:07Z","department":[{"_id":"NiBa"}],"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:45:01Z","citation":{"ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","short":"T. Ellis, (2018).","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95."}},{"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","keyword":["microscopy","microfluidics"],"status":"public","_id":"5569","article_processing_charge":"No","publist_id":"7385","author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Nikolic","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"}],"file_date_updated":"2020-07-14T12:47:04Z","department":[{"_id":"CaGu"}],"title":"Time-lapse microscopy data","citation":{"short":"T. Bergmiller, N. Nikolic, (2018).","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74","mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74."},"date_updated":"2024-02-21T13:44:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["579"],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:35Z","doi":"10.15479/AT:ISTA:74","date_published":"2018-02-07T00:00:00Z","related_material":{"record":[{"relation":"research_paper","id":"438","status":"public"}]},"datarep_id":"74","year":"2018","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5637","checksum":"61ebb92213cfffeba3ddbaff984b81af","creator":"system","file_size":3558703796,"date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","date_created":"2018-12-12T13:04:39Z"},{"file_size":1830422606,"date_updated":"2020-07-14T12:47:04Z","creator":"system","file_name":"IST-2018-74-v1+3_15-07-31.zip","date_created":"2018-12-12T13:04:55Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_id":"5638","checksum":"bf26649af310ef6892d68576515cde6d"},{"file_id":"5639","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","date_created":"2018-12-12T13:05:11Z","file_size":2140849248,"date_updated":"2020-07-14T12:47:04Z","creator":"system"}],"day":"07"},{"date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41467-018-05417-9","date_created":"2018-12-11T11:44:57Z","isi":1,"has_accepted_license":"1","year":"2018","day":"30","publication":"Nature Communications","publisher":"Springer Nature","quality_controlled":"1","oa":1,"author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"last_name":"Mc","full_name":"Mc, Andersson Anna","first_name":"Andersson Anna"},{"last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"publist_id":"7760","article_processing_charge":"No","external_id":{"isi":["000440149300021"]},"title":"Statistical mechanics for metabolic networks during steady state growth","citation":{"chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-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"}],"article_number":"2988","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5587"}]},"issue":"1","volume":9,"ec_funded":1,"publication_status":"published","file":[{"file_size":1043205,"date_updated":"2020-07-14T12:45:06Z","creator":"dernst","file_name":"2018_NatureComm_DeMartino.pdf","date_created":"2018-12-17T16:44:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","file_id":"5728"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 9","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"oa_version":"Published Version","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:06Z","date_updated":"2024-02-21T13:45:39Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"161"},{"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:08Z","article_processing_charge":"No","author":[{"orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"date_updated":"2024-02-21T13:45:39Z","citation":{"mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.","apa":"De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","short":"D. De Martino, G. Tkačik, (2018).","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62.","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62."},"keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","_id":"5587","ec_funded":1,"date_created":"2018-12-12T12:31:41Z","date_published":"2018-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:62","related_material":{"record":[{"relation":"research_paper","id":"161","status":"public"}]},"file":[{"file_id":"5641","checksum":"97992e3e8cf8544ec985a48971708726","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"IST-2018-111-v1+1_CODES.zip","date_created":"2018-12-12T13:05:13Z","file_size":14376,"date_updated":"2020-07-14T12:47:08Z","creator":"system"}],"day":"21","year":"2018","datarep_id":"111","has_accepted_license":"1","month":"09","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).","lang":"eng"}]},{"page":"365 - 375","date_created":"2018-12-11T11:47:04Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1534/genetics.117.300513","year":"2018","has_accepted_license":"1","isi":1,"publication":"Genetics","day":"01","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","external_id":{"isi":["000419356300024"]},"article_processing_charge":"No","publist_id":"7274","author":[{"first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","citation":{"ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","apa":"Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300513","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"ec_funded":1,"issue":"1","volume":208,"related_material":{"record":[{"id":"5571","status":"public","relation":"popular_science"},{"relation":"popular_science","status":"public","id":"5572"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"2123845e7031a0cf043905be160f9e69","file_id":"5132","date_updated":"2020-07-14T12:46:50Z","file_size":1311661,"creator":"system","date_created":"2018-12-12T10:15:14Z","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf"}],"scopus_import":"1","intvolume":" 208","month":"01","abstract":[{"text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:50Z","department":[{"_id":"BeVi"}],"date_updated":"2024-02-21T13:48:27Z","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","pubrep_id":"1058","status":"public","_id":"542"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2018-12-18T13:22:58Z","date_published":"2018-06-14T00:00:00Z","doi":"10.1038/s42003-018-0078-7","year":"2018","has_accepted_license":"1","isi":1,"publication":"Communications Biology","day":"14","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"article_number":"71","article_processing_charge":"No","external_id":{"isi":["000461126500071"]},"author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","citation":{"ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7","mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 1","month":"06","abstract":[{"lang":"eng","text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures."}],"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"7196","status":"public"},{"status":"public","id":"5559","relation":"popular_science"}]},"volume":1,"issue":"1","publication_status":"published","publication_identifier":{"issn":["2399-3642"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2018_CommBiology_Pavlogiannis.pdf","date_created":"2018-12-18T13:37:04Z","file_size":1804194,"date_updated":"2020-07-14T12:47:10Z","creator":"dernst","file_id":"5752","checksum":"a9db825fa3b64a51ff3de035ec973b3e","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"1045","status":"public","_id":"5751","file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"KrCh"}],"date_updated":"2024-02-21T13:48:42Z","ddc":["004","519","576"]},{"ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:59:18Z","citation":{"ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","short":"C. Fraisse, (2018).","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757."},"file_date_updated":"2020-07-14T12:47:11Z","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","_id":"5757","status":"public","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"type":"research_data","day":"19","file":[{"checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"FileS1.zip","date_created":"2018-12-19T14:19:52Z","file_size":369837892,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse"},{"date_created":"2018-12-19T14:19:49Z","file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"creator":"cfraisse","checksum":"3592e467b4d8206650860b612d6e12f3","file_id":"5759","content_type":"application/zip","access_level":"open_access","relation":"main_file"},{"date_created":"2018-12-19T14:19:49Z","file_name":"FileS3.txt","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":881133,"file_id":"5760","checksum":"c37ac5d5437c457338afc128c1240655","access_level":"open_access","relation":"main_file","content_type":"text/plain"},{"checksum":"943dfd14da61817441e33e3e3cb8cdb9","file_id":"5761","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","file_size":883742,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse"},{"file_size":2495437,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS5.txt","date_created":"2018-12-19T14:19:49Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","file_id":"5762"},{"file_size":15913457,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS6.txt","date_created":"2018-12-19T14:19:50Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5763","checksum":"f40f661b987ca6fb6b47f650cbbb04e6"},{"creator":"cfraisse","file_size":2584120,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS7.txt","date_created":"2018-12-19T14:19:50Z","relation":"main_file","access_level":"open_access","content_type":"text/plain","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764"},{"content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5765","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_size":2446059,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS8.txt","date_created":"2018-12-19T14:19:50Z"},{"relation":"main_file","access_level":"open_access","content_type":"text/plain","file_id":"5766","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","creator":"cfraisse","file_size":100737,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS9.txt","date_created":"2018-12-19T14:19:50Z"}],"has_accepted_license":"1","year":"2018","related_material":{"record":[{"relation":"research_paper","status":"public","id":"6089"}]},"date_published":"2018-12-19T00:00:00Z","doi":"10.15479/at:ista:/5757","ec_funded":1,"contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"date_created":"2018-12-19T14:22:35Z","oa_version":"Published Version","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"month":"12","publisher":"Institute of Science and Technology Austria","oa":1},{"_id":"149","pubrep_id":"1040","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["515","519"],"date_updated":"2024-02-22T14:34:33Z","supervisor":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"}],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:44:57Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"month":"07","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"checksum":"d4dad55a7513f345706aaaba90cb1bb8","file_id":"6241","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_thesis_Alt.pdf","date_created":"2019-04-08T13:55:20Z","file_size":5801709,"date_updated":"2020-07-14T12:44:57Z","creator":"dernst"},{"creator":"dernst","file_size":3802059,"date_updated":"2020-07-14T12:44:57Z","file_name":"2018_thesis_Alt_source.zip","date_created":"2019-04-08T13:55:20Z","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"6242","checksum":"d73fcf46300dce74c403f2b491148ab4"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"id":"1677","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"550","status":"public"},{"status":"public","id":"6183","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"566","status":"public"},{"relation":"part_of_dissertation","id":"1010","status":"public"},{"id":"6240","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6184","relation":"part_of_dissertation"}]},"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040.","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","mla":"Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040","apa":"Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040"},"title":"Dyson equation and eigenvalue statistics of random matrices","article_processing_charge":"No","author":[{"first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","full_name":"Alt, Johannes"}],"publist_id":"7772","oa":1,"publisher":"Institute of Science and Technology Austria","day":"12","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:53Z","date_published":"2018-07-12T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1040","page":"456"},{"department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:01:59Z","type":"journal_article","article_type":"original","status":"public","_id":"415","ec_funded":1,"issue":"10","related_material":{"record":[{"status":"public","id":"10759","relation":"dissertation_contains"}]},"volume":148,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1711.09904","open_access":"1"}],"scopus_import":"1","intvolume":" 148","month":"03","abstract":[{"text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field.","lang":"eng"}],"oa_version":"Preprint","external_id":{"isi":["000427517200065"],"arxiv":["1711.09904"]},"article_processing_charge":"No","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7408","title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","citation":{"short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018.","apa":"Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591","mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.","ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307.","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"104307","date_created":"2018-12-11T11:46:21Z","date_published":"2018-03-14T00:00:00Z","doi":"10.1063/1.5017591","year":"2018","isi":1,"publication":"The Journal of Chemical Physics","day":"14","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n"},{"oa":1,"quality_controlled":"1","publisher":"ACM","publication":"ACM Transactions on Graphics","day":"30","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:48Z","date_published":"2018-07-30T00:00:00Z","doi":"10.1145/3197517.3201336","article_number":"94","project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336"},"title":"Water surface wavelets","external_id":{"isi":["000448185000055"]},"article_processing_charge":"No","author":[{"first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"full_name":"Skrivan, Tomas","last_name":"Skrivan","first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mueller Fischer, Matthias","last_name":"Mueller Fischer","first_name":"Matthias"},{"full_name":"Chentanez, Nuttapong","last_name":"Chentanez","first_name":"Nuttapong"},{"last_name":"Macklin","full_name":"Macklin, Miles","first_name":"Miles"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publist_id":"7789","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 37","month":"07","scopus_import":"1","alternative_title":["SIGGRAPH"],"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:44:45Z","file_size":22185016,"date_created":"2018-12-18T09:59:23Z","file_name":"2018_ACM_Jeschke.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"db75ebabe2ec432bf41389e614d6ef62","file_id":"5744"}],"publication_status":"published","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/"}]},"volume":37,"issue":"4","_id":"134","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","ddc":["000"],"date_updated":"2024-02-28T13:58:51Z","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:44:45Z"},{"article_number":"165301","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"}],"citation":{"ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301.","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"article_processing_charge":"No","author":[{"full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"last_name":"Tscherbul","full_name":"Tscherbul, Timur","first_name":"Timur"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2018","isi":1,"publication":"Physical Review Letters","day":"16","date_created":"2019-04-17T10:53:38Z","doi":"10.1103/physrevlett.121.165301","date_published":"2018-10-16T00:00:00Z","_id":"6339","type":"journal_article","status":"public","date_updated":"2024-02-28T13:15:09Z","department":[{"_id":"MiLe"}],"abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"scopus_import":"1","intvolume":" 121","month":"10","publication_status":"published","language":[{"iso":"eng"}],"issue":"16","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","relation":"press_release"}]},"volume":121},{"citation":{"chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"8025","author":[{"orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tscherbul","full_name":"Tscherbul, Timur","first_name":"Timur"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"external_id":{"arxiv":["1803.07990"]},"article_processing_charge":"No","title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","article_number":"165301","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"year":"2018","day":"16","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.121.165301","date_published":"2018-10-16T00:00:00Z","date_created":"2018-12-11T11:46:22Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"date_updated":"2024-02-28T13:14:53Z","department":[{"_id":"MiLe"}],"_id":"417","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":121,"issue":"16","abstract":[{"text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"month":"10","intvolume":" 121"},{"date_updated":"2024-03-27T23:30:06Z","ddc":["580"],"file_date_updated":"2022-05-23T09:12:38Z","department":[{"_id":"JiFr"}],"_id":"412","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2022-05-23T09:12:38Z","file_size":4407538,"date_created":"2022-05-23T09:12:38Z","file_name":"2018_PlantCell_Adamowski.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"4e165e653b67d3f0684697f21aace5a1","file_id":"11406","success":1}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6269"}]},"volume":30,"issue":"3","ec_funded":1,"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 30","citation":{"ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan"},{"first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula","last_name":"Kania"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"last_name":"De Jaeger","full_name":"De Jaeger, Geert","first_name":"Geert"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"7417","external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"article_processing_charge":"No","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"isi":1,"has_accepted_license":"1","year":"2018","day":"09","publication":"The Plant Cell","page":"700 - 716","date_published":"2018-04-09T00:00:00Z","doi":"10.1105/tpc.17.00785","date_created":"2018-12-11T11:46:20Z","acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1},{"scopus_import":"1","intvolume":" 5","month":"07","abstract":[{"text":"With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"4","related_material":{"record":[{"id":"6849","status":"public","relation":"dissertation_contains"}]},"volume":5,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"2018_ENeuro_Guerrero.pdf","date_created":"2019-02-05T12:48:36Z","file_size":3746884,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_id":"5921","checksum":"f4915d45fc7ad4648b7b7a13fdecca01","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"5914","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"JoCs"}],"date_updated":"2024-03-27T23:30:10Z","ddc":["570"],"oa":1,"publisher":"Society of Neuroscience","quality_controlled":"1","date_created":"2019-02-03T22:59:16Z","doi":"10.1523/ENEURO.0087-18.2018","date_published":"2018-07-27T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"eNeuro","day":"27","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"I2072-B27","name":"Interneuron plasticity during spatial learning","call_identifier":"FWF","_id":"257D4372-B435-11E9-9278-68D0E5697425"}],"article_number":"e0087","article_processing_charge":"No","external_id":{"isi":["000443994700007"]},"author":[{"last_name":"Rangel Guerrero","full_name":"Rangel Guerrero, Dámaris K","orcid":"0000-0002-8602-4374","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","first_name":"Dámaris K"},{"first_name":"James G.","last_name":"Donnett","full_name":"Donnett, James G."},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián","orcid":"0000-0001-6251-1007","full_name":"Kovács, Krisztián","last_name":"Kovács"}],"title":"Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning","citation":{"mla":"Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.","short":"D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).","ieee":"D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.","ama":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018","apa":"Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018","chicago":"Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.","ista":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"project":[{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"pmid":["29567714"],"isi":["000428043600047"]},"author":[{"full_name":"Brown, Markus","last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Assen","orcid":"0000-0003-3470-6119","full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P"},{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"first_name":"Helga","full_name":"Schachner, Helga","last_name":"Schachner"},{"full_name":"Asfour, Gabriele","last_name":"Asfour","first_name":"Gabriele"},{"last_name":"Bagó Horváth","full_name":"Bagó Horváth, Zsuzsanna","first_name":"Zsuzsanna"},{"first_name":"Jens","last_name":"Stein","full_name":"Stein, Jens"},{"first_name":"Pavel","last_name":"Uhrin","full_name":"Uhrin, Pavel"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho","first_name":"Dontscho"}],"publist_id":"7428","title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","citation":{"ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662","apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411.","ieee":"M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018.","mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662.","ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","page":"1408 - 1411","date_created":"2018-12-11T11:46:16Z","date_published":"2018-03-23T00:00:00Z","doi":"10.1126/science.aal3662","year":"2018","isi":1,"publication":"Science","day":"23","type":"journal_article","article_type":"original","status":"public","_id":"402","department":[{"_id":"MiSi"}],"date_updated":"2024-03-27T23:30:09Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aal3662"}],"scopus_import":"1","intvolume":" 359","month":"03","abstract":[{"text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":359,"issue":"6382","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6947"}]},"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_992.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","mla":"Tarlungeanu, Dora-Clara. The Branched Chain Amino Acids in Autism Spectrum Disorders . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_992.","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","apa":"Tarlungeanu, D.-C. (2018). The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:10.15479/AT:ISTA:th_992"},"title":"The branched chain amino acids in autism spectrum disorders ","article_processing_charge":"No","publist_id":"7434","author":[{"full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu","first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:46:14Z","doi":"10.15479/AT:ISTA:th_992","date_published":"2018-03-01T00:00:00Z","page":"88","_id":"395","pubrep_id":"992","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["570","616"],"date_updated":"2023-09-07T12:38:59Z","supervisor":[{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-02-11T23:30:15Z","department":[{"_id":"GaNo"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. ","lang":"eng"}],"month":"03","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"date_created":"2019-04-05T09:19:17Z","file_name":"2018_Thesis_Tarlungeanu_source.docx","creator":"dernst","date_updated":"2021-02-11T23:30:15Z","file_size":43684035,"file_id":"6217","checksum":"9f5231c96e0ad945040841a8630232da","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"embargo":"2018-03-15","file_id":"6218","checksum":"0c33c370aa2010df5c552db57a6d01e9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_Thesis_Tarlungeanu.pdf","date_created":"2019-04-05T09:19:17Z","creator":"dernst","file_size":30511532,"date_updated":"2021-02-11T11:17:16Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"1183","status":"public","relation":"part_of_dissertation"}]}},{"month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Asymmetries have long been known about in the central nervous system. From gross anatomical differences, such as the presence of the parapineal organ in only one hemisphere of the developing zebrafish, to more subtle differences in activity between both hemispheres, as seen in freely roaming animals or human participants under PET and fMRI imaging analysis. The presence of asymmetries has been demonstrated to have huge behavioural implications, with their disruption often leading to the generation of neurological disorders, memory problems, changes in personality, and in an organism's health and well-being. For my Ph.D. work I aimed to tackle two important avenues of research. The first being the process of input-side dependency in the hippocampus, with the goal of finding a key gene responsible for its development (Gene X). The second project was to do with experience-induced laterality formation in the hippocampus. Specifically, how laterality in the synapse density of the CA1 stratum radiatum (s.r.) could be induced purely through environmental enrichment. Through unilateral tracer injections into the CA3, I was able to selectively measure the properties of synapses within the CA1 and investigate how they differed based upon which hemisphere the presynaptic neurone originated. Having found the existence of a previously unreported reversed (left-isomerism) i.v. mutant, through morpholocal examination of labelled terminals in the CA1 s.r., I aimed to elucidate a key gene responsible for the process of left or right determination of inputs to the CA1 s.r.. This work relates to the previous finding of input-side dependent asymmetry in the wild-type rodent, where the origin of the projecting neurone to the CA1 will determine the morphology of a synapse, to a greater degree than the hemisphere in which the projection terminates. Using left- and right-isomerism i.v. mice, in combination with whole genome sequence analysis, I highlight Ena/VASP-like (Evl) as a potential target for Gene X. In relation to this topic, I also highlight my work in the recently published paper of how knockout of PirB can lead to a lack of input-side dependency in the murine hippocampus. For the second question, I show that the environmental enrichment paradigm will lead to an asymmetry in the synapse densities in the hippocampus of mice. I also highlight that the nature of the enrichment is of less consequence than the process of enrichment itself. I demonstrate that the CA3 region will dramatically alter its projection targets, in relation to environmental stimulation, with the asymmetry in synaptic density, caused by enrichment, relying heavily on commissural fibres. I also highlight the vital importance of input-side dependent asymmetry, as a necessary component of experience-dependent laterality formation in the CA1 s.r.. However, my results suggest that it isn't the only cause, as there appears to be a CA1 dependent mechanism also at play. Upon further investigation, I highlight the significant, and highly important, finding that the changes seen in the CA1 s.r. were predominantly caused through projections from the left-CA3, with the right-CA3 having less involvement in this mechanism."}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"682","status":"public"}]},"file":[{"creator":"dernst","date_updated":"2021-02-11T23:30:13Z","file_size":141270528,"date_created":"2019-04-09T07:16:26Z","file_name":"2018_Thesis_Case_Source.doc","access_level":"closed","relation":"source_file","content_type":"application/msword","embargo_to":"open_access","file_id":"6251","checksum":"dcc7b55619d8509dd62b8e99d6cdee44"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-07-05","file_id":"6252","checksum":"f69fdd5c8709c4e618aa8c1a1221153d","creator":"dernst","file_size":15193621,"date_updated":"2021-02-11T11:17:14Z","file_name":"2018_Thesis_Case.pdf","date_created":"2019-04-09T07:16:23Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","pubrep_id":"1032","type":"dissertation","_id":"51","file_date_updated":"2021-02-11T23:30:13Z","department":[{"_id":"RySh"}],"ddc":["571","576"],"supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:39:22Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2018-06-27T00:00:00Z","doi":"10.15479/AT:ISTA:th_1032","date_created":"2018-12-11T11:44:22Z","page":"186","day":"27","has_accepted_license":"1","year":"2018","title":"From the left to the right: A tale of asymmetries, environments, and hippocampal development","author":[{"first_name":"Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case","full_name":"Case, Matthew J"}],"publist_id":"8003","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. J. Case, “From the left to the right: A tale of asymmetries, environments, and hippocampal development,” Institute of Science and Technology Austria, 2018.","short":"M.J. Case, From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development, Institute of Science and Technology Austria, 2018.","apa":"Case, M. J. (2018). From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1032","ama":"Case MJ. From the left to the right: A tale of asymmetries, environments, and hippocampal development. 2018. doi:10.15479/AT:ISTA:th_1032","mla":"Case, Matthew J. From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1032.","ista":"Case MJ. 2018. From the left to the right: A tale of asymmetries, environments, and hippocampal development. Institute of Science and Technology Austria.","chicago":"Case, Matthew J. “From the Left to the Right: A Tale of Asymmetries, Environments, and Hippocampal Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1032."}},{"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2018","day":"21","page":"1 - 139","date_published":"2018-11-21T00:00:00Z","doi":"10.15479/AT:ISTA:th1057","date_created":"2018-12-11T11:44:08Z","citation":{"ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","apa":"Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:10.15479/AT:ISTA:th1057","mla":"Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8046","author":[{"first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","last_name":"Laukoter"}],"article_processing_charge":"No","title":"Role of genomic imprinting in cerebral cortex development","abstract":[{"lang":"eng","text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"dernst","date_updated":"2019-11-23T23:30:03Z","file_size":17949175,"date_created":"2019-05-10T07:47:04Z","file_name":"Thesis_LaukoterSusanne_FINAL.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"6396","checksum":"41fdbf5fdce312802935d88a8ad9932c"},{"date_updated":"2021-02-11T11:17:16Z","file_size":21187245,"creator":"dernst","date_created":"2019-05-10T07:47:04Z","file_name":"Thesis_LaukoterSusanne_FINAL.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"53001a9a0c9e570e598d861bb0af28aa","file_id":"6397","embargo":"2019-11-21"}],"language":[{"iso":"eng"}],"_id":"10","type":"dissertation","status":"public","pubrep_id":"1057","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"date_updated":"2023-09-07T12:40:44Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-02-11T11:17:16Z"},{"page":"99","date_created":"2018-12-11T11:45:49Z","doi":"10.15479/AT:ISTA:th_998","date_published":"2018-04-12T00:00:00Z","year":"2018","has_accepted_license":"1","day":"12","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe best boss one can imagine. I would also like to thank all current and past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m proud that I could be part of it. Furthermore, I would like to say ‘thank you’ to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to Federica Benvenuti for being part of my committee. I am also grateful to Jack \r\nMerrin in the nanofabrication facility and all the people working in the bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","article_processing_charge":"No","publist_id":"7542","author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"}],"title":"Branched actin networks in dendritic cell biology","citation":{"chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_998.","ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria.","mla":"Leithner, Alexander F. Branched Actin Networks in Dendritic Cell Biology. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_998.","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018.","apa":"Leithner, A. F. (2018). Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_998","ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:10.15479/AT:ISTA:th_998"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"part_of_dissertation","id":"1321","status":"public"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","file_id":"6219","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2019-04-05T09:23:11Z","file_name":"PhD_thesis_AlexLeithner_final_version.docx","creator":"dernst","date_updated":"2021-02-11T23:30:17Z","file_size":29027671},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-04-15","checksum":"071f7476db29e41146824ebd0697cb10","file_id":"6220","creator":"dernst","file_size":66045341,"date_updated":"2021-02-11T11:17:16Z","file_name":"PhD_thesis_AlexLeithner.pdf","date_created":"2019-04-05T09:23:11Z"}],"alternative_title":["ISTA Thesis"],"month":"04","abstract":[{"text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Published Version","department":[{"_id":"MiSi"}],"file_date_updated":"2021-02-11T23:30:17Z","date_updated":"2023-09-07T12:39:44Z","supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"ddc":["571","599","610"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","pubrep_id":"998","status":"public","_id":"323"},{"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"2018_Hurny_thesis_source.docx","date_created":"2019-04-05T09:37:56Z","creator":"dernst","file_size":28112114,"date_updated":"2020-12-02T23:30:08Z","checksum":"0c9d6d1c80d9857e6e545213467bbcb2","file_id":"6226","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-07-10","checksum":"ecbe481a1413d270bd501b872c7ed54f","file_id":"6227","creator":"dernst","file_size":12524427,"date_updated":"2020-12-02T09:52:16Z","file_name":"2018_Hurny_thesis.pdf","date_created":"2019-04-05T09:37:55Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1024","status":"public"}]},"abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"01","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"date_updated":"2023-09-07T12:41:06Z","ddc":["570"],"department":[{"_id":"EvBe"}],"file_date_updated":"2020-12-02T23:30:08Z","_id":"539","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"930","has_accepted_license":"1","year":"2018","day":"01","page":"147","doi":"10.15479/AT:ISTA:th_930","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:03Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"mla":"Hurny, Andrej. Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_930.","apa":"Hurny, A. (2018). Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_930","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:10.15479/AT:ISTA:th_930","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_930.","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7277","author":[{"last_name":"Hurny","full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Andrej"}],"article_processing_charge":"No","title":"Identification and characterization of novel auxin-cytokinin cross-talk components"},{"title":"Reactivation content is important for consolidation of spatial memory","article_processing_charge":"No","author":[{"full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","last_name":"Gridchyn","first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8006","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Gridchyn, Igor. “Reactivation Content Is Important for Consolidation of Spatial Memory.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1042.","ista":"Gridchyn I. 2018. Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria.","mla":"Gridchyn, Igor. Reactivation Content Is Important for Consolidation of Spatial Memory. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1042.","ieee":"I. Gridchyn, “Reactivation content is important for consolidation of spatial memory,” Institute of Science and Technology Austria, 2018.","short":"I. Gridchyn, Reactivation Content Is Important for Consolidation of Spatial Memory, Institute of Science and Technology Austria, 2018.","ama":"Gridchyn I. Reactivation content is important for consolidation of spatial memory. 2018. doi:10.15479/AT:ISTA:th_1042","apa":"Gridchyn, I. (2018). Reactivation content is important for consolidation of spatial memory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1042"},"date_created":"2018-12-11T11:44:21Z","date_published":"2018-08-27T00:00:00Z","doi":"10.15479/AT:ISTA:th_1042","page":"104","day":"27","year":"2018","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T23:30:22Z","department":[{"_id":"JoCs"}],"ddc":["573"],"date_updated":"2023-09-07T12:42:44Z","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"pubrep_id":"1042","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"48","language":[{"iso":"eng"}],"file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"6236","checksum":"7db4415e435590fa33542c7b0a0321d7","file_size":7666687,"date_updated":"2021-02-11T23:30:22Z","creator":"dernst","file_name":"2018_Thesis_Gridchyn_source.docx","date_created":"2019-04-08T13:36:01Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-08-29","checksum":"f96f3fe8979f7b1e6db6acaca962b10c","file_id":"6237","creator":"dernst","file_size":6034153,"date_updated":"2021-02-11T11:17:18Z","file_name":"2018_Thesis_Gridchyn.pdf","date_created":"2019-04-08T13:36:01Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"08","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The hippocampus is a key brain region for spatial memory and navigation and is needed at all stages of memory, including encoding, consolidation, and recall. Hippocampal place cells selectively discharge at specific locations of the environment to form a cognitive map of the space. During the rest period and sleep following spatial navigation and/or learning, the waking activity of the place cells is reactivated within high synchrony events. This reactivation is thought to be important for memory consolidation and stabilization of the spatial representations. The aim of my thesis was to directly test whether the reactivation content encoded in firing patterns of place cells is important for consolidation of spatial memories. In particular, I aimed to test whether, in cases when multiple spatial memory traces are acquired during learning, the specific disruption of the reactivation of a subset of these memories leads to the selective disruption of the corresponding memory traces or through memory interference the other learned memories are disrupted as well. In this thesis, using a modified cheeseboard paradigm and a closed-loop recording setup with feedback optogenetic stimulation, I examined how the disruption of the reactivation of specific spiking patterns affects consolidation of the corresponding memory traces. To obtain multiple distinctive memories, animals had to perform a spatial task in two distinct cheeseboard environments and the reactivation of spiking patterns associated with one of the environments (target) was disrupted after learning during four hours rest period using a real-time decoding method. This real-time decoding method was capable of selectively affecting the firing rates and cofiring correlations of the target environment-encoding cells. The selective disruption led to behavioural impairment in the memory tests after the rest periods in the target environment but not in the other undisrupted control environment. In addition, the map of the target environment was less stable in the impaired memory tests compared to the learning session before than the map of the control environment. However, when the animal relearned the task, the same map recurred in the target environment that was present during learning before the disruption. Altogether my work demonstrated that the reactivation content is important: assembly-related disruption of reactivation can lead to a selective memory impairment and deficiency in map stability. These findings indeed suggest that reactivated assembly patterns reflect processes associated with the consolidation of memory traces. "}]},{"author":[{"first_name":"Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","full_name":"Belyaeva, Vera"}],"publist_id":"8047","article_processing_charge":"No","title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1064.","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","mla":"Belyaeva, Vera. Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1064.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:10.15479/AT:ISTA:th1064","apa":"Belyaeva, V. (2018). Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1064","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"96","doi":"10.15479/AT:ISTA:th1064","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:44:08Z","has_accepted_license":"1","year":"2018","day":"01","publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"DaSi"}],"file_date_updated":"2021-02-11T11:17:16Z","supervisor":[{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"date_updated":"2023-09-07T12:43:10Z","ddc":["570"],"type":"dissertation","status":"public","pubrep_id":"1064","_id":"9","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","file_id":"6243","date_updated":"2020-07-14T12:48:14Z","file_size":102737483,"creator":"dernst","date_created":"2019-04-08T14:13:12Z","file_name":"2018_Thesis_Belyaeva_source.docx"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","file_id":"6244","embargo":"2019-11-19","creator":"dernst","date_updated":"2021-02-11T11:17:16Z","file_size":88077843,"date_created":"2019-04-08T14:14:08Z","file_name":"2018_Thesis_Belyaeva.pdf"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"07","abstract":[{"text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it.","lang":"eng"}],"oa_version":"Published Version"},{"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","full_name":"Mckenzie, Catherine","last_name":"Mckenzie"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission . Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:th_1055.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:10.15479/at:ista:th_1055","apa":"Mckenzie, C. (2018). Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th_1055","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:th_1055.","ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/at:ista:th_1055","date_published":"2018-10-31T00:00:00Z","date_created":"2019-04-09T14:13:39Z","page":"95","day":"31","has_accepted_license":"1","year":"2018","status":"public","pubrep_id":"1055","type":"dissertation","_id":"6266","file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"HaJa"}],"ddc":["571","573"],"supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"date_updated":"2023-09-07T13:02:37Z","month":"10","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. ","lang":"eng"}],"related_material":{"record":[{"id":"7132","status":"public","relation":"new_edition"}]},"file":[{"date_created":"2019-04-09T14:12:40Z","file_name":"2018_Thesis_McKenzie.pdf","creator":"dernst","date_updated":"2021-02-11T11:17:16Z","file_size":4906420,"file_id":"6267","checksum":"9d2c2dca04b00e485470c28b262af59a","embargo":"2019-11-24","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"6268","checksum":"50b58c272899601bc6fd9642c4dc97f1","file_size":5053545,"date_updated":"2020-07-14T12:47:25Z","creator":"dernst","file_name":"2018_Thesis_McKenzie_source.docx","date_created":"2019-04-09T14:12:40Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD"},{"publisher":"Institute of Science and Technology Austria","oa":1,"page":"95","date_published":"2018-06-22T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1031","date_created":"2018-12-11T11:44:21Z","has_accepted_license":"1","year":"2018","day":"22","author":[{"last_name":"Capek","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8004","article_processing_charge":"No","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration","citation":{"mla":"Capek, Daniel. Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1031.","ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:10.15479/AT:ISTA:TH_1031","apa":"Capek, D. (2018). Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1031","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1031.","ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"1100","status":"public","relation":"part_of_dissertation"},{"id":"661","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"676","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-06-25","file_id":"6238","checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","creator":"dernst","file_size":31576521,"date_updated":"2021-02-11T11:17:17Z","file_name":"2018_Thesis_Capek.pdf","date_created":"2019-04-08T13:42:26Z"},{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","checksum":"876deb14067e638aba65d209668bd821","file_id":"6239","creator":"dernst","date_updated":"2021-02-11T23:30:21Z","file_size":38992956,"date_created":"2019-04-08T13:42:27Z","file_name":"2018_Thesis_Capek_source.docx"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","pubrep_id":"1031","_id":"50","file_date_updated":"2021-02-11T23:30:21Z","department":[{"_id":"CaHe"}],"supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:48:16Z","ddc":["570","591","596"]},{"_id":"26","status":"public","pubrep_id":"1059","type":"dissertation","ddc":["576","579"],"supervisor":[{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"date_updated":"2023-09-07T12:48:43Z","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:14Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"month":"10","alternative_title":["ISTA Thesis"],"file":[{"file_id":"5941","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Thesis_Steinrueck_final.docx","date_created":"2019-02-08T10:51:22Z","file_size":9190845,"date_updated":"2020-07-14T12:45:43Z","creator":"dernst"},{"embargo":"2019-11-02","file_id":"5942","checksum":"3def8b7854c8b42d643597ce0215efac","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_Steinrueck_final.pdf","date_created":"2019-02-08T10:51:22Z","creator":"dernst","file_size":7521973,"date_updated":"2021-02-11T11:17:14Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"704"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1059.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","mla":"Steinrück, Magdalena. The Influence of Sequence Context on the Evolution of Bacterial Gene Expression. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1059.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","apa":"Steinrück, M. (2018). The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1059","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:10.15479/AT:ISTA:th1059"},"title":"The influence of sequence context on the evolution of bacterial gene expression","author":[{"first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena","last_name":"Steinrück"}],"publist_id":"8029","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"30","has_accepted_license":"1","year":"2018","date_published":"2018-10-30T00:00:00Z","doi":"10.15479/AT:ISTA:th1059","date_created":"2018-12-11T11:44:14Z","page":"109"},{"date_updated":"2024-03-27T23:30:26Z","department":[{"_id":"GeKa"}],"_id":"5816","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["00346748"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"10058","relation":"dissertation_contains"}]},"volume":89,"issue":"11","abstract":[{"text":"Solid-state qubit manipulation and read-out fidelities are reaching fault-tolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signal-line bandwidth and fan-out problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an in-plane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.09522"}],"scopus_import":"1","intvolume":" 89","month":"11","citation":{"ama":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 2018;89(11). doi:10.1063/1.5038258","apa":"Hollmann, A., Jirovec, D., Kucharski, M., Kissinger, D., Fischer, G., & Schreiber, L. R. (2018). 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. AIP Publishing. https://doi.org/10.1063/1.5038258","short":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, L.R. Schreiber, Review of Scientific Instruments 89 (2018).","ieee":"A. Hollmann, D. Jirovec, M. Kucharski, D. Kissinger, G. Fischer, and L. R. Schreiber, “30 GHz-voltage controlled oscillator operating at 4 K,” Review of Scientific Instruments, vol. 89, no. 11. AIP Publishing, 2018.","mla":"Hollmann, Arne, et al. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments, vol. 89, no. 11, 114701, AIP Publishing, 2018, doi:10.1063/1.5038258.","ista":"Hollmann A, Jirovec D, Kucharski M, Kissinger D, Fischer G, Schreiber LR. 2018. 30 GHz-voltage controlled oscillator operating at 4 K. Review of Scientific Instruments. 89(11), 114701.","chicago":"Hollmann, Arne, Daniel Jirovec, Maciej Kucharski, Dietmar Kissinger, Gunter Fischer, and Lars R. Schreiber. “30 GHz-Voltage Controlled Oscillator Operating at 4 K.” Review of Scientific Instruments. AIP Publishing, 2018. https://doi.org/10.1063/1.5038258."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000451735700054"],"arxiv":["1804.09522"]},"author":[{"first_name":"Arne","full_name":"Hollmann, Arne","last_name":"Hollmann"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec"},{"first_name":"Maciej","last_name":"Kucharski","full_name":"Kucharski, Maciej"},{"first_name":"Dietmar","full_name":"Kissinger, Dietmar","last_name":"Kissinger"},{"full_name":"Fischer, Gunter","last_name":"Fischer","first_name":"Gunter"},{"last_name":"Schreiber","full_name":"Schreiber, Lars R.","first_name":"Lars R."}],"title":"30 GHz-voltage controlled oscillator operating at 4 K","article_number":"114701","year":"2018","isi":1,"publication":"Review of Scientific Instruments","day":"01","date_created":"2019-01-10T14:22:23Z","doi":"10.1063/1.5038258","date_published":"2018-11-01T00:00:00Z","oa":1,"publisher":"AIP Publishing","quality_controlled":"1"},{"file":[{"creator":"dernst","file_size":5656866,"date_updated":"2021-02-11T11:17:17Z","file_name":"2018_Thesis_Lukacisinova.pdf","date_created":"2019-04-09T13:49:24Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2020-01-25","checksum":"fc60585c9eaad868ac007004ef130908","file_id":"6264"},{"date_created":"2019-04-09T13:49:23Z","file_name":"2018_Thesis_Lukacisinova_source.docx","creator":"dernst","date_updated":"2020-07-14T12:47:25Z","file_size":5168054,"checksum":"264057ec0a92ab348cc83b41f021ba92","file_id":"6265","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"1619","status":"public"},{"relation":"part_of_dissertation","id":"696","status":"public"},{"relation":"part_of_dissertation","id":"1027","status":"public"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Antibiotic resistance can emerge spontaneously through genomic mutation and render treatment ineffective. To counteract this process, in addition to the discovery and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its determinantsis needed. To address this challenge, this thesisuncoversnew genetic determinants of resistance evolvability using a customized robotic setup, exploressystematic ways in which resistance evolution is perturbed due to dose-responsecharacteristics of drugs and mutation rate differences,and mathematically investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We find severalgenes which strongly inhibit or potentiate resistance evolution. In order to identify them, we first developedan automated high-throughput feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds of cultures by dynamically re-diluting the cultures and adjusting the antibiotic concentration. We implementedthis protocol on a customized liquid handling robot and propagated 100 different gene deletion strains of Escherichia coliin triplicate for over 100 generations in tetracycline and in chloramphenicol, and comparedtheir adaptation rates.We find a diminishing returns pattern, where initially sensitive strains adapted more compared to less sensitive ones. Our data uncover that deletions of certain genes which do not affect mutation rate,including efflux pump components, a chaperone and severalstructural and regulatory genes can strongly and reproducibly alterresistance evolution. Sequencing analysis of evolved populations indicates that epistasis with resistance mutations is the most likelyexplanation. This work could inspire treatment strategies in which targeted inhibitors of evolvability mechanisms will be given alongside antibiotics to slow down resistance evolution and extend theefficacy of antibiotics.We implemented astochasticpopulation genetics model, toverifyways in which general properties, namely, dose-response characteristics of drugs and mutation rates, influence evolutionary dynamics. In particular, under the exposure to antibiotics with shallow dose-response curves,bacteria have narrower distributions of fitness effects of new mutations. We show that in silicothis also leads to slower resistance evolution. We see and confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge of these patterns can aid in predicting the dynamics of antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on a previously described type of evolvability modifier –a stress-induced mutagenesis allele –we find conditions under which it can persist in a population under periodic selectionakin to clinical treatment. We set up a deterministic infinite populationcontinuous time model tracking the frequencies of a mutator and resistance allele and evaluate various treatment schemes in how well they maintain a stress-induced mutator allele. In particular,a high diversity of stresses is crucial for the persistence of the mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which are likely to decrease levels of resistance could lead to stronger selection of highly evolvable genotypes.In the long run, this work will lead to a deeper understanding of the genetic and cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. "}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"month":"12","alternative_title":["ISTA Thesis"],"ddc":["570","576","579"],"supervisor":[{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-22T09:20:37Z","file_date_updated":"2021-02-11T11:17:17Z","department":[{"_id":"ToBo"}],"_id":"6263","status":"public","type":"dissertation","day":"28","has_accepted_license":"1","year":"2018","date_published":"2018-12-28T00:00:00Z","doi":"10.15479/AT:ISTA:th1072","date_created":"2019-04-09T13:57:15Z","page":"91","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1072.","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","mla":"Lukacisinova, Marta. Genetic Determinants of Antibiotic Resistance Evolution. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th1072.","ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","apa":"Lukacisinova, M. (2018). Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1072","ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:10.15479/AT:ISTA:th1072"},"title":"Genetic determinants of antibiotic resistance evolution","author":[{"last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"date_created":"2018-12-11T11:47:05Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1534/g3.117.300452","page":"845 - 857","publication":"G3: Genes, Genomes, Genetics","day":"01","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","article_processing_charge":"No","external_id":{"isi":["000426693300011"]},"author":[{"last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek","full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389"},{"first_name":"Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","last_name":"Ratheesh","full_name":"Ratheesh, Aparna","orcid":"0000-0001-7190-0776"},{"last_name":"Valosková","full_name":"Valosková, Katarina","first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Belyaeva, Vera","last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera"},{"first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","full_name":"Wachner, Stephanie","last_name":"Wachner"},{"first_name":"Yutaka","last_name":"Matsubayashi","full_name":"Matsubayashi, Yutaka"},{"first_name":"Besaiz","last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz"},{"last_name":"Stramer","full_name":"Stramer, Brian","first_name":"Brian"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7271","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:10.1534/g3.117.300452.","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.117.300452","ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 2018;8(3):845-857. doi:10.1534/g3.117.300452","short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","ieee":"A. György et al., “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” G3: Genes, Genomes, Genetics, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” G3: Genes, Genomes, Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/g3.117.300452.","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857."},"project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen","grant_number":"P29638"},{"call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638"},{"name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","grant_number":"LSC16-021 ","_id":"2637E9C0-B435-11E9-9278-68D0E5697425"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"}],"ec_funded":1,"volume":8,"related_material":{"record":[{"relation":"research_paper","id":"6530"},{"relation":"research_paper","id":"6543"},{"relation":"dissertation_contains","status":"public","id":"11193"},{"status":"public","id":"6546","relation":"dissertation_contains"}]},"issue":"3","language":[{"iso":"eng"}],"file":[{"file_id":"4905","checksum":"7d9d28b915159078a4ca7add568010e8","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:48Z","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","creator":"system","date_updated":"2020-07-14T12:46:56Z","file_size":2251222}],"publication_status":"published","intvolume":" 8","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult."}],"acknowledged_ssus":[{"_id":"LifeSc"}],"file_date_updated":"2020-07-14T12:46:56Z","department":[{"_id":"DaSi"}],"ddc":["570"],"date_updated":"2024-03-27T23:30:29Z","pubrep_id":"990","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"544"},{"volume":223,"issue":"3","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"ec_funded":1,"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:47:20Z","file_size":5542926,"date_created":"2018-12-12T10:15:36Z","file_name":"IST-2018-1013-v1+1_2018_Kleindienst_Differential.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5157","checksum":"a55b3103476ecb5f4f983d8801807e8b"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 223","abstract":[{"lang":"eng","text":"Metabotropic GABAB receptors mediate slow inhibitory effects presynaptically and postsynaptically through the modulation of different effector signalling pathways. Here, we analysed the distribution of GABAB receptors using highly sensitive SDS-digested freeze-fracture replica labelling in mouse cerebellar Purkinje cells. Immunoreactivity for GABAB1 was observed on presynaptic and, more abundantly, on postsynaptic compartments, showing both scattered and clustered distribution patterns. Quantitative analysis of immunoparticles revealed a somato-dendritic gradient, with the density of immunoparticles increasing 26-fold from somata to dendritic spines. To understand the spatial relationship of GABAB receptors with two key effector ion channels, the G protein-gated inwardly rectifying K+ (GIRK/Kir3) channel and the voltage-dependent Ca2+ channel, biochemical and immunohistochemical approaches were performed. Co-immunoprecipitation analysis demonstrated that GABAB receptors co-assembled with GIRK and CaV2.1 channels in the cerebellum. Using double-labelling immunoelectron microscopic techniques, co-clustering between GABAB1 and GIRK2 was detected in dendritic spines, whereas they were mainly segregated in the dendritic shafts. In contrast, co-clustering of GABAB1 and CaV2.1 was detected in dendritic shafts but not spines. Presynaptically, although no significant co-clustering of GABAB1 and GIRK2 or CaV2.1 channels was detected, inter-cluster distance for GABAB1 and GIRK2 was significantly smaller in the active zone than in the dendritic shafts, and that for GABAB1 and CaV2.1 was significantly smaller in the active zone than in the dendritic shafts and spines. Thus, GABAB receptors are associated with GIRK and CaV2.1 channels in different subcellular compartments. These data provide a better framework for understanding the different roles played by GABAB receptors and their effector ion channels in the cerebellar network."}],"oa_version":"Published Version","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:20Z","date_updated":"2024-03-27T23:30:30Z","ddc":["571"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"1013","_id":"612","page":"1565 - 1587","doi":"10.1007/s00429-017-1568-y","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:47:29Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Brain Structure and Function","publisher":"Springer","quality_controlled":"1","oa":1,"author":[{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"first_name":"Francisco","last_name":"Ciruela","full_name":"Ciruela, Francisco"},{"full_name":"Cózar, Javier","last_name":"Cózar","first_name":"Javier"},{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David","last_name":"Kleindienst"},{"first_name":"Luis","full_name":"De La Ossa, Luis","last_name":"De La Ossa"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"last_name":"Wickman","full_name":"Wickman, Kevin","first_name":"Kevin"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"}],"publist_id":"7192","article_processing_charge":"No","external_id":{"isi":["000428419500030"]},"title":"Differential association of GABAB receptors with their effector ion channels in Purkinje cells","citation":{"chicago":"Luján, Rafael, Carolina Aguado, Francisco Ciruela, Javier Cózar, David Kleindienst, Luis De La Ossa, Bernhard Bettler, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function. Springer, 2018. https://doi.org/10.1007/s00429-017-1568-y.","ista":"Luján R, Aguado C, Ciruela F, Cózar J, Kleindienst D, De La Ossa L, Bettler B, Wickman K, Watanabe M, Shigemoto R, Fukazawa Y. 2018. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 223(3), 1565–1587.","mla":"Luján, Rafael, et al. “Differential Association of GABAB Receptors with Their Effector Ion Channels in Purkinje Cells.” Brain Structure and Function, vol. 223, no. 3, Springer, 2018, pp. 1565–87, doi:10.1007/s00429-017-1568-y.","ama":"Luján R, Aguado C, Ciruela F, et al. Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. 2018;223(3):1565-1587. doi:10.1007/s00429-017-1568-y","apa":"Luján, R., Aguado, C., Ciruela, F., Cózar, J., Kleindienst, D., De La Ossa, L., … Fukazawa, Y. (2018). Differential association of GABAB receptors with their effector ion channels in Purkinje cells. Brain Structure and Function. Springer. https://doi.org/10.1007/s00429-017-1568-y","ieee":"R. Luján et al., “Differential association of GABAB receptors with their effector ion channels in Purkinje cells,” Brain Structure and Function, vol. 223, no. 3. Springer, pp. 1565–1587, 2018.","short":"R. Luján, C. Aguado, F. Ciruela, J. Cózar, D. Kleindienst, L. De La Ossa, B. Bettler, K. Wickman, M. Watanabe, R. Shigemoto, Y. Fukazawa, Brain Structure and Function 223 (2018) 1565–1587."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"21","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:28Z","date_updated":"2024-03-27T23:30:31Z","ddc":["570"],"scopus_import":"1","intvolume":" 9","month":"11","abstract":[{"text":"Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":9,"issue":"1","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"6363"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":4651930,"date_updated":"2020-07-14T12:45:28Z","file_name":"2018_NatureComm_Espinoza.pdf","date_created":"2018-12-17T15:41:57Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5715","checksum":"9fe2a63bd95a5067d896c087d07998f3"}],"project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"article_number":"4605","external_id":{"isi":["000449069700009"]},"article_processing_charge":"No","publist_id":"8034","author":[{"id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia ","last_name":"Espinoza Martinez","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia "},{"last_name":"Guzmán","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José"},{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Xiaomin","last_name":"Zhang"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","citation":{"chicago":"Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06899-3.","ista":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605.","mla":"Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” Nature Communications, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06899-3.","ama":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-06899-3","apa":"Espinoza Martinez, C., Guzmán, J., Zhang, X., & Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06899-3","ieee":"C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J..","date_created":"2018-12-11T11:44:12Z","date_published":"2018-11-02T00:00:00Z","doi":"10.1038/s41467-018-06899-3","year":"2018","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"02"},{"_id":"66","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CONCUR: Conference on Concurrency Theory","location":"Beijing, China","end_date":"2018-09-07","start_date":"2018-09-04"},"ddc":["000"],"date_updated":"2024-03-27T23:30:33Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:34Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions."}],"month":"09","intvolume":" 118","alternative_title":["LIPIcs"],"scopus_import":"1","file":[{"file_id":"5696","checksum":"68a055b1aaa241cc38375083cf832a7d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_CONCUR_Chatterjee.pdf","date_created":"2018-12-17T12:08:00Z","creator":"dernst","file_size":1078309,"date_updated":"2020-07-14T12:47:34Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-95977-087-3"]},"publication_status":"published","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"volume":118,"ec_funded":1,"article_number":"11","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic mean-payoff games for the analysis of attacks in crypto-currencies,” presented at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Velner, Y. (2018). Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol. 118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.11","mla":"Chatterjee, Krishnendu, et al. Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.11.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 118, 11.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.11."},"title":"Ergodic mean-payoff games for the analysis of attacks in crypto-currencies","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","last_name":"Goharshady"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"publist_id":"7988","external_id":{"arxiv":["1806.03108"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"day":"01","has_accepted_license":"1","year":"2018","doi":"10.4230/LIPIcs.CONCUR.2018.11","date_published":"2018-09-01T00:00:00Z","date_created":"2018-12-11T11:44:27Z"},{"quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"The research was partially supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games).","page":"739 - 767","date_published":"2018-04-01T00:00:00Z","doi":"10.1007/978-3-319-89884-1_26","date_created":"2018-12-11T11:45:45Z","has_accepted_license":"1","year":"2018","day":"01","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"publist_id":"7554","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","last_name":"Goharshady"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"article_processing_charge":"No","title":"Quantitative analysis of smart contracts","citation":{"mla":"Chatterjee, Krishnendu, et al. Quantitative Analysis of Smart Contracts. Vol. 10801, Springer, 2018, pp. 739–67, doi:10.1007/978-3-319-89884-1_26.","apa":"Chatterjee, K., Goharshady, A. K., & Velner, Y. (2018). Quantitative analysis of smart contracts (Vol. 10801, pp. 739–767). Presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89884-1_26","ama":"Chatterjee K, Goharshady AK, Velner Y. Quantitative analysis of smart contracts. In: Vol 10801. Springer; 2018:739-767. doi:10.1007/978-3-319-89884-1_26","ieee":"K. Chatterjee, A. K. Goharshady, and Y. Velner, “Quantitative analysis of smart contracts,” presented at the ESOP: European Symposium on Programming, Thessaloniki, Greece, 2018, vol. 10801, pp. 739–767.","short":"K. Chatterjee, A.K. Goharshady, Y. Velner, in:, Springer, 2018, pp. 739–767.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Yaron Velner. “Quantitative Analysis of Smart Contracts,” 10801:739–67. Springer, 2018. https://doi.org/10.1007/978-3-319-89884-1_26.","ista":"Chatterjee K, Goharshady AK, Velner Y. 2018. Quantitative analysis of smart contracts. ESOP: European Symposium on Programming, LNCS, vol. 10801, 739–767."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"scopus_import":"1","month":"04","intvolume":" 10801","abstract":[{"lang":"eng","text":"Smart contracts are computer programs that are executed by a network of mutually distrusting agents, without the need of an external trusted authority. Smart contracts handle and transfer assets of considerable value (in the form of crypto-currency like Bitcoin). Hence, it is crucial that their implementation is bug-free. We identify the utility (or expected payoff) of interacting with such smart contracts as the basic and canonical quantitative property for such contracts. We present a framework for such quantitative analysis of smart contracts. Such a formal framework poses new and novel research challenges in programming languages, as it requires modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior and modeling utilities which are not specified as standard temporal properties such as safety and termination. While game-theoretic incentives have been analyzed in the security community, their analysis has been restricted to the very special case of stateless games. However, to analyze smart contracts, stateful analysis is required as it must account for the different program states of the protocol. Our main contributions are as follows: we present (i)~a simplified programming language for smart contracts; (ii)~an automatic translation of the programs to state-based games; (iii)~an abstraction-refinement approach to solve such games; and (iv)~experimental results on real-world-inspired smart contracts."}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"volume":10801,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-17T15:45:49Z","file_name":"2018_ESOP_Chatterjee.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:00Z","file_size":1394993,"checksum":"9c8a8338c571903b599b6ca93abd2cce","file_id":"5716","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"ESOP: European Symposium on Programming","start_date":"2018-04-16","location":"Thessaloniki, Greece","end_date":"2018-04-19"},"status":"public","_id":"311","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:00Z","date_updated":"2024-03-27T23:30:33Z","ddc":["000"]},{"publication_status":"published","publication_identifier":{"isbn":["978-1-5386-7975-3 "]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b25c9bb7cf6e7e6634e692d26d41ead8","file_id":"6341","file_size":624338,"date_updated":"2020-07-14T12:47:27Z","creator":"akafshda","file_name":"blockchain2018.pdf","date_created":"2019-04-18T10:36:39Z"}],"ec_funded":1,"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"We present a secure approach for maintaining andreporting credit history records on the Blockchain. Our ap-proach removes third-parties such as credit reporting agen-cies from the lending process and replaces them with smartcontracts. This allows customers to interact directly with thelenders or banks while ensuring the integrity, unmalleabilityand privacy of their credit data. Additionally, each customerhas full control over complete or selective disclosure of hercredit records, eliminating the risk of privacy violations or databreaches. Moreover, our approach provides strong guaranteesfor the lenders as well. A lender can check both correctness andcompleteness of the credit data disclosed to her. This is the firstapproach that can perform all credit reporting tasks withouta central authority or changing the financial mechanisms*."}],"oa_version":"Submitted Version","scopus_import":"1","month":"09","date_updated":"2024-03-27T23:30:34Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:27Z","department":[{"_id":"KrCh"}],"_id":"6340","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"conference":{"end_date":"2018-08-03","location":"Halifax, Canada","start_date":"2018-07-30","name":"IEEE International Conference on Blockchain"},"type":"conference","status":"public","year":"2018","isi":1,"has_accepted_license":"1","publication":"Proceedings of the IEEE International Conference on Blockchain","day":"01","page":"1343-1348","date_created":"2019-04-18T10:37:35Z","doi":"10.1109/Cybermatics_2018.2018.00231","date_published":"2018-09-01T00:00:00Z","oa":1,"publisher":"IEEE","quality_controlled":"1","citation":{"ama":"Goharshady AK, Behrouz A, Chatterjee K. Secure Credit Reporting on the Blockchain. In: Proceedings of the IEEE International Conference on Blockchain. IEEE; 2018:1343-1348. doi:10.1109/Cybermatics_2018.2018.00231","apa":"Goharshady, A. K., Behrouz, A., & Chatterjee, K. (2018). Secure Credit Reporting on the Blockchain. In Proceedings of the IEEE International Conference on Blockchain (pp. 1343–1348). Halifax, Canada: IEEE. https://doi.org/10.1109/Cybermatics_2018.2018.00231","short":"A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–1348.","ieee":"A. K. Goharshady, A. Behrouz, and K. Chatterjee, “Secure Credit Reporting on the Blockchain,” in Proceedings of the IEEE International Conference on Blockchain, Halifax, Canada, 2018, pp. 1343–1348.","mla":"Goharshady, Amir Kafshdar, et al. “Secure Credit Reporting on the Blockchain.” Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–48, doi:10.1109/Cybermatics_2018.2018.00231.","ista":"Goharshady AK, Behrouz A, Chatterjee K. 2018. Secure Credit Reporting on the Blockchain. Proceedings of the IEEE International Conference on Blockchain. IEEE International Conference on Blockchain, 1343–1348.","chicago":"Goharshady, Amir Kafshdar, Ali Behrouz, and Krishnendu Chatterjee. “Secure Credit Reporting on the Blockchain.” In Proceedings of the IEEE International Conference on Blockchain, 1343–48. IEEE, 2018. https://doi.org/10.1109/Cybermatics_2018.2018.00231."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000481634500196"],"arxiv":["1805.09104"]},"article_processing_charge":"No","author":[{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"},{"first_name":"Ali","full_name":"Behrouz, Ali","last_name":"Behrouz"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"title":"Secure Credit Reporting on the Blockchain","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3, 9, Association for Computing Machinery (ACM), 2018, doi:10.1145/3210257.","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 3. Association for Computing Machinery (ACM), 2018.","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 40 (2018).","ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 2018;40(3). doi:10.1145/3210257","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2018). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3210257","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3210257.","ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2018. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. ACM Transactions on Programming Languages and Systems. 40(3), 9."},"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"article_processing_charge":"No","external_id":{"arxiv":["1510.07565"],"isi":["000444694800001"]},"article_number":"9","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"day":"01","publication":"ACM Transactions on Programming Languages and Systems","isi":1,"year":"2018","doi":"10.1145/3210257","date_published":"2018-08-01T00:00:00Z","date_created":"2019-02-14T14:31:52Z","quality_controlled":"1","publisher":"Association for Computing Machinery (ACM)","oa":1,"date_updated":"2024-03-27T23:30:34Z","department":[{"_id":"KrCh"}],"_id":"6009","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0164-0925"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"1437","relation":"earlier_version"},{"id":"5441","status":"public","relation":"earlier_version"},{"status":"public","id":"5442","relation":"earlier_version"},{"relation":"dissertation_contains","id":"8934","status":"public"}]},"issue":"3","volume":40,"ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"We study algorithmic questions wrt algebraic path properties in concurrent systems, where the transitions of the system are labeled from a complete, closed semiring. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.\r\n","lang":"eng"}],"month":"08","intvolume":" 40","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1510.07565","open_access":"1"}]},{"date_created":"2019-02-13T13:26:27Z","doi":"10.24963/ijcai.2018/653","date_published":"2018-07-17T00:00:00Z","page":"4700-4707","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","day":"17","year":"2018","isi":1,"oa":1,"publisher":"IJCAI","quality_controlled":"1","title":"Computational approaches for stochastic shortest path on succinct MDPs","article_processing_charge":"No","external_id":{"isi":["000764175404118"],"arxiv":["1804.08984"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"first_name":"Nastaran","full_name":"Okati, Nastaran","last_name":"Okati"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Chatterjee K, Fu H, Goharshady AK, Okati N. 2018. Computational approaches for stochastic shortest path on succinct MDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4700–4707.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Nastaran Okati. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018:4700–4707. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/653.","ama":"Chatterjee K, Fu H, Goharshady AK, Okati N. Computational approaches for stochastic shortest path on succinct MDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018. IJCAI; 2018:4700-4707. doi:10.24963/ijcai.2018/653","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Okati, N. (2018). Computational approaches for stochastic shortest path on succinct MDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018, pp. 4700–4707). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/653","short":"K. Chatterjee, H. Fu, A.K. Goharshady, N. Okati, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4700–4707.","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and N. Okati, “Computational approaches for stochastic shortest path on succinct MDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4700–4707.","mla":"Chatterjee, Krishnendu, et al. “Computational Approaches for Stochastic Shortest Path on Succinct MDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018, IJCAI, 2018, pp. 4700–07, doi:10.24963/ijcai.2018/653."},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"volume":2018,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["10450823"],"isbn":["978-099924112-7"]},"intvolume":" 2018","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08984"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the stochastic shortest path (SSP)problem for succinct Markov decision processes(MDPs), where the MDP consists of a set of vari-ables, and a set of nondeterministic rules that up-date the variables. First, we show that several ex-amples from the AI literature can be modeled assuccinct MDPs. Then we present computationalapproaches for upper and lower bounds for theSSP problem: (a) for computing upper bounds, ourmethod is polynomial-time in the implicit descrip-tion of the MDP; (b) for lower bounds, we present apolynomial-time (in the size of the implicit descrip-tion) reduction to quadratic programming. Our ap-proach is applicable even to infinite-state MDPs.Finally, we present experimental results to demon-strate the effectiveness of our approach on severalclassical examples from the AI literature."}],"department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:34Z","status":"public","conference":{"location":"Stockholm, Sweden","end_date":"2018-07-19","start_date":"2018-07-13","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"type":"conference","_id":"5977"},{"project":[{"grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","last_name":"Kühnen"},{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","last_name":"Scarselli"},{"last_name":"Schaner","full_name":"Schaner, Markus","first_name":"Markus","id":"316CE034-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"publist_id":"7401","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000433113900004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942.","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” Flow Turbulence and Combustion, vol. 100, no. 4. Springer, pp. 919–942, 2018.","ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 2018;100(4):919-942. doi:10.1007/s10494-018-9896-4","apa":"Kühnen, J., Scarselli, D., Schaner, M., & Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. Springer. https://doi.org/10.1007/s10494-018-9896-4","mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:10.1007/s10494-018-9896-4.","ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” Flow Turbulence and Combustion. Springer, 2018. https://doi.org/10.1007/s10494-018-9896-4."},"publisher":"Springer","quality_controlled":"1","oa":1,"doi":"10.1007/s10494-018-9896-4","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:46:23Z","page":"919 - 942","day":"01","publication":"Flow Turbulence and Combustion","isi":1,"has_accepted_license":"1","year":"2018","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"422","file_date_updated":"2020-07-14T12:46:25Z","department":[{"_id":"BjHo"}],"ddc":["530"],"date_updated":"2024-03-27T23:30:36Z","month":"01","intvolume":" 100","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle.","lang":"eng"}],"volume":100,"related_material":{"record":[{"status":"public","id":"7258","relation":"dissertation_contains"}]},"issue":"4","ec_funded":1,"file":[{"creator":"dernst","file_size":2210020,"date_updated":"2020-07-14T12:46:25Z","file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","date_created":"2018-12-17T15:52:37Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"d7c0bade150faabca150b0a9986e60ca","file_id":"5717"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":14,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"id":"14530","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"7258"}]},"abstract":[{"text":"Turbulence is the major cause of friction losses in transport processes and it is responsible for a drastic drag increase in flows over bounding surfaces. While much effort is invested into developing ways to control and reduce turbulence intensities, so far no methods exist to altogether eliminate turbulence if velocities are sufficiently large. We demonstrate for pipe flow that appropriate distortions to the velocity profile lead to a complete collapse of turbulence and subsequently friction losses are reduced by as much as 90%. Counterintuitively, the return to laminar motion is accomplished by initially increasing turbulence intensities or by transiently amplifying wall shear. Since neither the Reynolds number nor the shear stresses decrease (the latter often increase), these measures are not indicative of turbulence collapse. Instead, an amplification mechanism measuring the interaction between eddies and the mean shear is found to set a threshold below which turbulence is suppressed beyond recovery.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.06543"}],"scopus_import":"1","intvolume":" 14","month":"01","date_updated":"2024-03-27T23:30:36Z","department":[{"_id":"BjHo"}],"_id":"461","type":"journal_article","status":"public","year":"2018","isi":1,"publication":"Nature Physics","day":"08","page":"386-390","date_created":"2018-12-11T11:46:36Z","date_published":"2018-01-08T00:00:00Z","doi":"10.1038/s41567-017-0018-3","acknowledgement":"We acknowledge the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 737549) and the Deutsche Forschungsgemeinschaft (Project No. FOR 1182) for financial support. We thank our technician P. Maier for providing highly valuable ideas and greatly supporting us in all technical aspects. We thank M. Schaner for technical drawings, construction and design. We thank M. Schwegel for a Matlab code to post-process experimental data.","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","citation":{"mla":"Kühnen, Jakob, et al. “Destabilizing Turbulence in Pipe Flow.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 386–90, doi:10.1038/s41567-017-0018-3.","ieee":"J. Kühnen et al., “Destabilizing turbulence in pipe flow,” Nature Physics, vol. 14. Nature Publishing Group, pp. 386–390, 2018.","short":"J. Kühnen, B. Song, D. Scarselli, N.B. Budanur, M. Riedl, A. Willis, M. Avila, B. Hof, Nature Physics 14 (2018) 386–390.","apa":"Kühnen, J., Song, B., Scarselli, D., Budanur, N. B., Riedl, M., Willis, A., … Hof, B. (2018). Destabilizing turbulence in pipe flow. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-017-0018-3","ama":"Kühnen J, Song B, Scarselli D, et al. Destabilizing turbulence in pipe flow. Nature Physics. 2018;14:386-390. doi:10.1038/s41567-017-0018-3","chicago":"Kühnen, Jakob, Baofang Song, Davide Scarselli, Nazmi B Budanur, Michael Riedl, Ashley Willis, Marc Avila, and Björn Hof. “Destabilizing Turbulence in Pipe Flow.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-017-0018-3.","ista":"Kühnen J, Song B, Scarselli D, Budanur NB, Riedl M, Willis A, Avila M, Hof B. 2018. Destabilizing turbulence in pipe flow. Nature Physics. 14, 386–390."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000429434100020"]},"author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","last_name":"Kühnen","full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179"},{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","last_name":"Scarselli","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Riedl","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311"},{"full_name":"Willis, Ashley","last_name":"Willis","first_name":"Ashley"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publist_id":"7360","title":"Destabilizing turbulence in pipe flow","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"737549","name":"Eliminating turbulence in oil pipelines"}]},{"_id":"449","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"967","status":"public","date_updated":"2024-03-27T23:30:37Z","ddc":["581"],"file_date_updated":"2020-07-14T12:46:30Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 14","month":"01","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","date_created":"2018-12-12T10:10:52Z","creator":"system","file_size":24709062,"date_updated":"2020-07-14T12:46:30Z","file_id":"4843","checksum":"0276d66788ec076f4924164a39e6a712","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1127"},{"relation":"dissertation_contains","status":"public","id":"7172"},{"relation":"dissertation_contains","status":"public","id":"8822"}]},"volume":14,"issue":"1","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"citation":{"ieee":"T. Prat et al., “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no. 1. Public Library of Science, 2018.","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007177","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1). doi:10.1371/journal.pgen.1007177","mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007177.","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1).","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes","external_id":{"isi":["000423718600034"]},"publist_id":"7373","author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat","full_name":"Prat, Tomas"},{"last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub"},{"first_name":"Wim","full_name":"Grunewald, Wim","last_name":"Grunewald"},{"full_name":"Vasileva, Mina K","last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K"},{"full_name":"Molnar, Gergely","last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"first_name":"Markus","full_name":"Schmid, Markus","last_name":"Schmid"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","year":"2018","isi":1,"has_accepted_license":"1","publication":"PLoS Genetics","day":"29","date_created":"2018-12-11T11:46:32Z","date_published":"2018-01-29T00:00:00Z","doi":"10.1371/journal.pgen.1007177"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5714","checksum":"266b03f4fb8198e83141617aaa99dcab","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T15:38:56Z","file_name":"2018_ScientificReports_Grones.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:20Z","file_size":2413876}],"ec_funded":1,"volume":8,"issue":"1","related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]},"abstract":[{"text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"07","date_updated":"2024-03-27T23:30:37Z","ddc":["581"],"file_date_updated":"2020-07-14T12:45:20Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"_id":"191","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","year":"2018","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"06","date_created":"2018-12-11T11:45:06Z","doi":"10.1038/s41598-018-28188-1","date_published":"2018-07-06T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"ieee":"P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., & Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1.","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000437673200053"]},"article_processing_charge":"No","author":[{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","full_name":"Abas, Melinda F","last_name":"Abas"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny"},{"last_name":"Jones","full_name":"Jones, Angharad","first_name":"Angharad"},{"last_name":"Waidmann","full_name":"Waidmann, Sascha","first_name":"Sascha"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"7729","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","article_number":"10279","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}]},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}]},"volume":87,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 87","month":"01","abstract":[{"lang":"eng","text":"Plant hormones as signalling molecules play an essential role in the control of plant growth and development. Typically, sites of hormonal action are usually distant from the site of biosynthesis thus relying on efficient transport mechanisms. Over the last decades, molecular identification of proteins and protein complexes involved in hormonal transport has started. Advanced screens for genes involved in hormonal transport in combination with transport assays using heterologous systems such as yeast, insect, or tobacco BY2 cells or Xenopus oocytes provided important insights into mechanisms underlying distribution of hormones in plant body and led to identification of principal transporters for each hormone. This review gives a short overview of the mechanisms of hormonal transport and transporters identified in Arabidopsis thaliana."}],"oa_version":"None","department":[{"_id":"EvBe"}],"date_updated":"2024-03-27T23:30:39Z","type":"journal_article","status":"public","_id":"47","page":"115 - 138","date_created":"2018-12-11T11:44:20Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1016/bs.abr.2018.09.007","year":"2018","isi":1,"publication":"Advances in Botanical Research","day":"01","quality_controlled":"1","publisher":"Elsevier","external_id":{"isi":["000453657800006"]},"article_processing_charge":"No","publist_id":"8007","author":[{"last_name":"Abualia","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Lacombe","full_name":"Lacombe, Benoît","first_name":"Benoît"}],"title":"Transporters and mechanisms of hormone transport in arabidopsis","citation":{"mla":"Abualia, Rashed, et al. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” Advances in Botanical Research, vol. 87, Elsevier, 2018, pp. 115–38, doi:10.1016/bs.abr.2018.09.007.","short":"R. Abualia, E. Benková, B. Lacombe, Advances in Botanical Research 87 (2018) 115–138.","ieee":"R. Abualia, E. Benková, and B. Lacombe, “Transporters and mechanisms of hormone transport in arabidopsis,” Advances in Botanical Research, vol. 87. Elsevier, pp. 115–138, 2018.","ama":"Abualia R, Benková E, Lacombe B. Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. 2018;87:115-138. doi:10.1016/bs.abr.2018.09.007","apa":"Abualia, R., Benková, E., & Lacombe, B. (2018). Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. Elsevier. https://doi.org/10.1016/bs.abr.2018.09.007","chicago":"Abualia, Rashed, Eva Benková, and Benoît Lacombe. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” Advances in Botanical Research. Elsevier, 2018. https://doi.org/10.1016/bs.abr.2018.09.007.","ista":"Abualia R, Benková E, Lacombe B. 2018. Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. 87, 115–138."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"15","status":"public","type":"journal_article","date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux."}],"acknowledged_ssus":[{"_id":"SSU"}],"month":"05","intvolume":" 19","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":19,"issue":"6","related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"ec_funded":1,"project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"},{"name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425"},{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616.","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41590-018-0109-z.","ieee":"M. Hons et al., “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” Nature Immunology, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.","apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/s41590-018-0109-z","ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 2018;19(6):606-616. doi:10.1038/s41590-018-0109-z","mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:10.1038/s41590-018-0109-z."},"title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","author":[{"full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348","last_name":"Hons","first_name":"Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","last_name":"Gärtner"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"full_name":"Stein, Jens","last_name":"Stein","first_name":"Jens"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8040","external_id":{"isi":["000433041500026"],"pmid":["29777221"]},"article_processing_charge":"No","acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"18","publication":"Nature Immunology","isi":1,"year":"2018","date_published":"2018-05-18T00:00:00Z","doi":"10.1038/s41590-018-0109-z","date_created":"2018-12-11T11:44:10Z","page":"606 - 616"},{"article_processing_charge":"No","external_id":{"isi":["000446548100012"]},"author":[{"last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"title":"Incorrect trafficking route leads to autism","citation":{"ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” Brain a journal of neurology, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018.","short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","apa":"Contreras, X., & Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. Brain a Journal of Neurology. Oxford University Press. https://doi.org/10.1093/brain/awy218","ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. Brain a journal of neurology. 2018;141(9):2542-2544. doi:10.1093/brain/awy218","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” Brain a Journal of Neurology, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:10.1093/brain/awy218.","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” Brain a Journal of Neurology. Oxford University Press, 2018. https://doi.org/10.1093/brain/awy218."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"2542 - 2544","date_created":"2018-12-11T11:44:14Z","date_published":"2018-09-01T00:00:00Z","doi":"10.1093/brain/awy218","year":"2018","isi":1,"publication":"Brain a journal of neurology","day":"01","quality_controlled":"1","publisher":"Oxford University Press","department":[{"_id":"SiHi"}],"date_updated":"2024-03-27T23:30:41Z","type":"journal_article","status":"public","_id":"28","volume":141,"related_material":{"record":[{"id":"7902","status":"public","relation":"part_of_dissertation"}]},"issue":"9","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 141","month":"09","abstract":[{"text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. ","lang":"eng"}],"oa_version":"None"},{"publist_id":"7381","author":[{"last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","citation":{"ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685.","ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018.","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685","apa":"Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.21769/BioProtoc.2685","date_published":"2018-01-05T00:00:00Z","date_created":"2018-12-11T11:46:30Z","has_accepted_license":"1","year":"2018","day":"05","publication":"Bio-protocol","quality_controlled":"1","publisher":"Bio-protocol","oa":1,"acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","department":[{"_id":"JiFr"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:46:29Z","date_updated":"2024-03-27T23:30:42Z","ddc":["576","581"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"970","_id":"442","volume":8,"related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"issue":"1","ec_funded":1,"publication_identifier":{"eissn":["2331-8325"]},"publication_status":"published","file":[{"file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","date_created":"2018-12-12T10:17:43Z","file_size":11352389,"date_updated":"2020-07-14T12:46:29Z","creator":"system","file_id":"5299","checksum":"6644ba698206eda32b0abf09128e63e3","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"month":"01","intvolume":" 8","abstract":[{"text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH.","lang":"eng"}],"oa_version":"Published Version"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience. Nature Publishing Group, 2018. https://doi.org/10.1038/s41593-018-0266-2.","ista":"Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727.","mla":"Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:10.1038/s41593-018-0266-2.","short":"E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727.","ieee":"E. Deliu et al., “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” Nature Neuroscience, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018.","apa":"Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/s41593-018-0266-2","ama":"Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 2018;21(12):1717-1727. doi:10.1038/s41593-018-0266-2"},"title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","article_processing_charge":"No","external_id":{"isi":["000451324700010"]},"author":[{"id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Deliu","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena"},{"first_name":"Niccoló","last_name":"Arecco","full_name":"Arecco, Niccoló"},{"full_name":"Morandell, Jasmin","last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter"},{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"full_name":"Girardot, Charles","last_name":"Girardot","first_name":"Charles"},{"first_name":"Eva","full_name":"Käsper, Eva","last_name":"Käsper"},{"full_name":"Kozlova, Alena","last_name":"Kozlova","id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D","first_name":"Alena"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","last_name":"Kishi","full_name":"Kishi, Kasumi"},{"first_name":"Ilaria","id":"B6467F20-02D0-11E9-BDA5-E960C241894A","orcid":"0000-0002-9529-4464","full_name":"Chiaradia, Ilaria","last_name":"Chiaradia"},{"last_name":"Noh","full_name":"Noh, Kyung","first_name":"Kyung"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8054","project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"}],"publication":"Nature Neuroscience","day":"19","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:05Z","date_published":"2018-11-19T00:00:00Z","doi":"10.1038/s41593-018-0266-2","page":"1717 - 1727","acknowledgement":"This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N.","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","ddc":["570"],"date_updated":"2024-03-27T23:30:44Z","file_date_updated":"2020-07-14T12:45:58Z","department":[{"_id":"GaNo"},{"_id":"EdHa"}],"_id":"3","pubrep_id":"1071","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6255","checksum":"60abd0f05b7cdc08a6b0ec460884084f","file_size":8167169,"date_updated":"2020-07-14T12:45:58Z","creator":"dernst","file_name":"2017_NatureNeuroscience_Deliu.pdf","date_created":"2019-04-09T07:41:57Z"}],"publication_status":"published","volume":21,"issue":"12","related_material":{"record":[{"status":"public","id":"6074","relation":"popular_science"},{"relation":"dissertation_contains","status":"public","id":"12364"}],"link":[{"url":"https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/","relation":"press_release","description":"News on IST Homepage"}]},"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder."}],"intvolume":" 21","month":"11","scopus_import":"1"},{"issue":"48","related_material":{"record":[{"relation":"dissertation_contains","id":"10293","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/"}]},"volume":115,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320","open_access":"1"}],"month":"11","intvolume":" 115","abstract":[{"text":"Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"KrCh"}],"date_updated":"2024-03-27T23:30:44Z","type":"journal_article","status":"public","_id":"2","page":"12241-12246","doi":"10.1073/pnas.1810565115","date_published":"2018-11-27T00:00:00Z","date_created":"2018-12-11T11:44:05Z","isi":1,"year":"2018","day":"27","publication":"PNAS","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"isi":["000451351000063"],"pmid":["30429320"]},"title":"Indirect reciprocity with private, noisy, and incomplete information","citation":{"ama":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246. doi:10.1073/pnas.1810565115","apa":"Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246.","ieee":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018.","mla":"Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:10.1073/pnas.1810565115.","ista":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.","chicago":"Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]},{"title":"Evolutionary potential of transcription factors for gene regulatory rewiring","author":[{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler"},{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"publist_id":"7987","external_id":{"isi":["000447947600021"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y","mla":"Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"},{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41559-018-0651-y","date_published":"2018-09-10T00:00:00Z","date_created":"2018-12-11T11:44:27Z","page":"1633 - 1643","day":"10","publication":"Nature Ecology and Evolution","has_accepted_license":"1","isi":1,"year":"2018","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"ddc":["570"],"date_updated":"2024-03-27T23:30:48Z","status":"public","type":"journal_article","article_type":"original","_id":"67","issue":"10","volume":2,"related_material":{"record":[{"status":"public","id":"5585","relation":"popular_science"},{"relation":"dissertation_contains","id":"6371","status":"public"}]},"ec_funded":1,"file":[{"file_size":1135973,"date_updated":"2020-07-14T12:47:37Z","creator":"dernst","file_name":"2018_NatureEcology_Igler.pdf","date_created":"2020-05-14T11:28:52Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7830","checksum":"383a2e2c944a856e2e821ec8e7bf71b6"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 2","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution."}]},{"file":[{"checksum":"1435781526c77413802adee0d4583cce","file_id":"5611","access_level":"open_access","relation":"main_file","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","date_created":"2018-12-12T13:02:45Z","file_name":"IST-2018-108-v1+1_data_figures.xlsx","creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":16507}],"day":"20","datarep_id":"108","year":"2018","has_accepted_license":"1","date_created":"2018-12-12T12:31:40Z","ec_funded":1,"date_published":"2018-07-20T00:00:00Z","doi":"10.15479/AT:ISTA:108","related_material":{"record":[{"relation":"research_paper","status":"public","id":"67"},{"status":"public","id":"6371","relation":"research_paper"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mean repression values and standard error of the mean are given for all operator mutant libraries."}],"month":"07","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108","mla":"Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108."},"date_updated":"2024-03-27T23:30:48Z","file_date_updated":"2020-07-14T12:47:07Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","article_processing_charge":"No","author":[{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler"},{"full_name":"Lagator, Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"_id":"5585","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573"}],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data"},{"issue":"32","volume":10,"publication_status":"published","file":[{"file_id":"6968","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-10-24T11:38:14Z","file_name":"2017_Physics_Fink.pdf","creator":"dernst","date_updated":"2019-10-24T11:38:14Z","file_size":193622}],"language":[{"iso":"eng"}],"month":"03","intvolume":" 10","abstract":[{"text":"From microwave ovens to satellite television to the GPS and data services on our mobile phones, microwave technology is everywhere today. But one technology that has so far failed to prove its worth in this wavelength regime is quantum communication that uses the states of single photons as information carriers. This is because single microwave photons, as opposed to classical microwave signals, are extremely vulnerable to noise from thermal excitations in the channels through which they travel. Two new independent studies, one by Ze-Liang Xiang at Technische Universität Wien (Vienna), Austria, and colleagues [1] and another by Benoît Vermersch at the University of Innsbruck, also in Austria, and colleagues [2] now describe a theoretical protocol for microwave quantum communication that is resilient to thermal and other types of noise. Their approach could become a powerful technique to establish fast links between superconducting data processors in a future all-microwave quantum network.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"JoFi"}],"file_date_updated":"2019-10-24T11:38:14Z","date_updated":"2022-06-07T10:58:31Z","ddc":["530"],"article_type":"review","type":"journal_article","status":"public","_id":"1013","date_published":"2017-03-27T00:00:00Z","doi":"10.1103/Physics.10.32","date_created":"2018-12-11T11:49:41Z","has_accepted_license":"1","year":"2017","day":"27","publication":"Physics","quality_controlled":"1","publisher":"American Physical Society","oa":1,"author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"publist_id":"6382","article_processing_charge":"No","title":"Viewpoint: Microwave quantum states beat the heat","citation":{"mla":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics, vol. 10, no. 32, American Physical Society, 2017, doi:10.1103/Physics.10.32.","ieee":"J. M. Fink, “Viewpoint: Microwave quantum states beat the heat,” Physics, vol. 10, no. 32. American Physical Society, 2017.","short":"J.M. Fink, Physics 10 (2017).","apa":"Fink, J. M. (2017). Viewpoint: Microwave quantum states beat the heat. Physics. American Physical Society. https://doi.org/10.1103/Physics.10.32","ama":"Fink JM. Viewpoint: Microwave quantum states beat the heat. Physics. 2017;10(32). doi:10.1103/Physics.10.32","chicago":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics. American Physical Society, 2017. https://doi.org/10.1103/Physics.10.32.","ista":"Fink JM. 2017. Viewpoint: Microwave quantum states beat the heat. Physics. 10(32)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 2","month":"12","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158121"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"volume":2,"issue":"POPL","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2475-1421"]},"status":"public","conference":{"start_date":"2018-01-07","location":"Los Angeles, CA, United States","end_date":"2018-01-13","name":"POPL: Programming Languages"},"type":"journal_article","article_type":"original","_id":"10418","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-12-07T08:04:14Z","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","date_created":"2021-12-05T23:01:49Z","date_published":"2017-12-07T00:00:00Z","doi":"10.1145/3158121","publication":"Proceedings of the ACM on Programming Languages","day":"07","year":"2017","article_number":"33","title":"A new proof rule for almost-sure termination","external_id":{"arxiv":["1711.03588"]},"article_processing_charge":"No","author":[{"first_name":"Annabelle","last_name":"Mciver","full_name":"Mciver, Annabelle"},{"first_name":"Carroll","full_name":"Morgan, Carroll","last_name":"Morgan"},{"first_name":"Benjamin Lucien","last_name":"Kaminski","full_name":"Kaminski, Benjamin Lucien"},{"first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen","full_name":"Katoen, Joost P"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.","mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121.","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121","apa":"Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121"}},{"date_created":"2018-12-11T11:50:12Z","doi":"10.1145/3040718.3040729","date_published":"2017-01-12T00:00:00Z","page":"3 - 11","language":[{"iso":"eng"}],"publication":"Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms","day":"12","year":"2017","publication_status":"published","publication_identifier":{"isbn":["978-145034651-1"]},"month":"01","quality_controlled":"1","scopus_import":1,"publisher":"ACM","oa_version":"None","abstract":[{"lang":"eng","text":"There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes)."}],"department":[{"_id":"NiBa"}],"title":"An application of stochastic differential equations to evolutionary algorithms","publist_id":"6255","author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729","ama":"Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729","ieee":"T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.","short":"T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.","mla":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.","ista":"Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.","chicago":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729."},"date_updated":"2021-01-12T06:48:22Z","status":"public","conference":{"name":"FOGA: Foundations of Genetic Algorithms","location":"Copenhagen, Denmark","end_date":"2017-01-15","start_date":"2017-01-12"},"type":"conference","_id":"1112"},{"file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:48:51Z","ddc":["005","600"],"type":"conference","conference":{"start_date":"2017-01-09","location":"Berkeley, CA, United States","end_date":"2017-01-11","name":"ITCS: Innovations in Theoretical Computer Science"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"927","_id":"1175","volume":67,"publication_identifier":{"issn":["18688969"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5263","checksum":"dbc94810be07c2fb1945d5c2a6130e6c","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_size":557769,"date_created":"2018-12-12T10:17:11Z","file_name":"IST-2018-927-v1+1_LIPIcs-ITCS-2017-38.pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["LIPIcs"],"month":"01","intvolume":" 67","abstract":[{"lang":"eng","text":"We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure."}],"oa_version":"Published Version","publist_id":"6179","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"last_name":"De Rezende","full_name":"De Rezende, Susanna","first_name":"Susanna"},{"full_name":"Nordstrom, Jakob","last_name":"Nordstrom","first_name":"Jakob"},{"first_name":"Marc","last_name":"Vinyals","full_name":"Vinyals, Marc"}],"title":"Cumulative space in black-white pebbling and resolution","editor":[{"last_name":"Papadimitriou","full_name":"Papadimitriou, Christos","first_name":"Christos"}],"citation":{"ista":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. 2017. Cumulative space in black-white pebbling and resolution. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 67, 38:1-38-21.","chicago":"Alwen, Joel F, Susanna De Rezende, Jakob Nordstrom, and Marc Vinyals. “Cumulative Space in Black-White Pebbling and Resolution.” edited by Christos Papadimitriou, 67:38:1-38-21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ITCS.2017.38.","short":"J.F. Alwen, S. De Rezende, J. Nordstrom, M. Vinyals, in:, C. Papadimitriou (Ed.), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21.","ieee":"J. F. Alwen, S. De Rezende, J. Nordstrom, and M. Vinyals, “Cumulative space in black-white pebbling and resolution,” presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States, 2017, vol. 67, p. 38:1-38-21.","ama":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. Cumulative space in black-white pebbling and resolution. In: Papadimitriou C, ed. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:38:1-38-21. doi:10.4230/LIPIcs.ITCS.2017.38","apa":"Alwen, J. F., De Rezende, S., Nordstrom, J., & Vinyals, M. (2017). Cumulative space in black-white pebbling and resolution. In C. Papadimitriou (Ed.) (Vol. 67, p. 38:1-38-21). Presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2017.38","mla":"Alwen, Joel F., et al. Cumulative Space in Black-White Pebbling and Resolution. Edited by Christos Papadimitriou, vol. 67, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21, doi:10.4230/LIPIcs.ITCS.2017.38."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"38:1-38-21","date_published":"2017-01-01T00:00:00Z","doi":"10.4230/LIPIcs.ITCS.2017.38","date_created":"2018-12-11T11:50:33Z","has_accepted_license":"1","year":"2017","day":"01","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1},{"date_created":"2018-12-11T11:50:38Z","date_published":"2017-03-01T00:00:00Z","doi":"10.1007/s11538-016-0244-3","page":"525-559","publication":"Bulletin of Mathematical Biology","day":"01","year":"2017","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","title":"Existence of traveling waves for the generalized F–KPP equation","author":[{"first_name":"Richard","full_name":"Kollár, Richard","last_name":"Kollár"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","full_name":"Novak, Sebastian"}],"publist_id":"6160","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3.","apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3.","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559."},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"ec_funded":1,"issue":"3","volume":79,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 79","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00944"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed.","lang":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:48:58Z","status":"public","type":"journal_article","_id":"1191"},{"status":"public","pubrep_id":"782","type":"journal_article","_id":"1211","file_date_updated":"2020-07-14T12:44:39Z","department":[{"_id":"BjHo"}],"ddc":["530"],"date_updated":"2021-01-12T06:49:07Z","month":"05","intvolume":" 167","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.","lang":"eng"}],"volume":167,"issue":"3-4","file":[{"date_created":"2018-12-12T10:18:01Z","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","date_updated":"2020-07-14T12:44:39Z","file_size":2820207,"creator":"system","file_id":"5319","checksum":"3e971d09eb167761aa0888ed415b0056","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","publist_id":"6136","author":[{"first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur"},{"last_name":"Cvitanović","full_name":"Cvitanović, Predrag","first_name":"Predrag"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z.","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:10.1007/s10955-016-1672-z.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z","apa":"Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655, 2017."},"quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","date_published":"2017-05-01T00:00:00Z","doi":"10.1007/s10955-016-1672-z","date_created":"2018-12-11T11:50:44Z","page":"636-655","day":"01","publication":"Journal of Statistical Physics","has_accepted_license":"1","year":"2017"},{"publisher":"Brown University","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Graph Algorithms and Applications","has_accepted_license":"1","year":"2017","doi":"10.7155/jgaa.00408","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:50:13Z","page":"135 - 154","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408.","ista":"Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154.","mla":"Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154."},"title":"Hanani-Tutte for radial planarity","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"last_name":"Pelsmajer","full_name":"Pelsmajer, Michael","first_name":"Michael"},{"last_name":"Schaefer","full_name":"Schaefer, Marcus","first_name":"Marcus"}],"publist_id":"6254","external_id":{"arxiv":["1608.08662"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth."}],"month":"01","intvolume":" 21","scopus_import":1,"file":[{"file_size":573623,"date_updated":"2019-10-24T10:54:37Z","creator":"dernst","file_name":"2017_JournalGraphAlgorithms_Fulek.pdf","date_created":"2019-10-24T10:54:37Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"6967"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"1164","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"1595"}]},"volume":21,"issue":"1","ec_funded":1,"_id":"1113","status":"public","type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-02-23T10:05:57Z","file_date_updated":"2019-10-24T10:54:37Z","department":[{"_id":"UlWa"}]},{"editor":[{"last_name":"Wikström","full_name":"Wikström, Mårten","first_name":"Mårten"}],"department":[{"_id":"LeSa"}],"title":"Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions","author":[{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"publist_id":"7379","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025","apa":"Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025","short":"L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59.","ieee":"L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.","mla":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:10.1039/9781788010405-00025.","ista":"Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59.","chicago":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025."},"date_updated":"2021-01-12T07:56:59Z","status":"public","type":"book_chapter","_id":"444","series_title":"Mechanisms of Primary Energy Transduction in Biology ","doi":"10.1039/9781788010405-00025","date_published":"2017-11-29T00:00:00Z","date_created":"2018-12-11T11:46:30Z","page":"25 - 59","day":"29","language":[{"iso":"eng"}],"publication":"Mechanisms of primary energy transduction in biology ","publication_identifier":{"isbn":["978-1-78262-865-1"]},"year":"2017","publication_status":"published","month":"11","quality_controlled":"1","publisher":"Royal Society of Chemistry","oa_version":"None","abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations."}]},{"publication_status":"published","file":[{"creator":"system","file_size":977192,"date_updated":"2020-07-14T12:46:31Z","file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf","date_created":"2018-12-12T10:14:03Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"99a2474088e20ac74b1882c4fbbb45b1","file_id":"5052"}],"language":[{"iso":"eng"}],"volume":113,"issue":"9","abstract":[{"text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.","lang":"eng"}],"oa_version":"Published Version","month":"11","intvolume":" 113","date_updated":"2021-01-12T07:59:28Z","ddc":["570"],"department":[{"_id":"MaLo"}],"file_date_updated":"2020-07-14T12:46:31Z","_id":"453","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"965","has_accepted_license":"1","year":"2017","day":"07","publication":"Biophysical Journal","page":"2055 - 2067","doi":"10.1016/j.bpj.2017.09.006","date_published":"2017-11-07T00:00:00Z","date_created":"2018-12-11T11:46:33Z","acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ","quality_controlled":"1","publisher":"Biophysical Society","oa":1,"citation":{"mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006.","ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006","apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006","ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006.","ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. 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We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years."}],"oa_version":"Published Version","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"}],"publist_id":"7357","external_id":{"arxiv":["1410.0833"]},"article_processing_charge":"No","title":"Improved algorithms for parity and Streett objectives","citation":{"mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017.","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017).","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017.","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"article_number":"26","date_published":"2017-09-26T00:00:00Z","doi":"10.23638/LMCS-13(3:26)2017","date_created":"2018-12-11T11:46:37Z","has_accepted_license":"1","year":"2017","day":"26","publication":"Logical Methods in Computer Science","publisher":"International Federation of Computational Logic","quality_controlled":"1","oa":1},{"date_created":"2018-12-11T11:46:39Z","date_published":"2017-07-01T00:00:00Z","doi":"10.1145/3072959.3073678","publication":"ACM Transactions on Graphics","day":"01","year":"2017","has_accepted_license":"1","oa":1,"publisher":"ACM","quality_controlled":"1","title":"Water wave packets","article_processing_charge":"Yes (in subscription journal)","publist_id":"7350","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).","ieee":"S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017.","ama":"Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678","apa":"Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678.","ista":"Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103."},"project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"article_number":"103","ec_funded":1,"volume":36,"issue":"4","language":[{"iso":"eng"}],"file":[{"file_id":"7359","checksum":"82a3b2bfeee4ddef16ecc21675d1a48a","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-01-24T09:32:35Z","file_name":"wavepackets_final.pdf","date_updated":"2020-07-14T12:46:34Z","file_size":13131683,"creator":"wojtan"}],"publication_status":"published","publication_identifier":{"issn":["07300301"]},"intvolume":" 36","month":"07","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:46:34Z","ddc":["006"],"date_updated":"2023-02-23T12:20:26Z","status":"public","article_type":"original","type":"journal_article","_id":"470"},{"_id":"471","status":"public","type":"journal_article","date_updated":"2023-02-21T16:48:11Z","department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. "}],"intvolume":" 18","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.05739"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["15293785"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"1234","relation":"earlier_version"}]},"volume":18,"issue":"2","article_number":"12","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). 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Petrov, “Faster statistical model checking for unbounded temporal properties,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2. ACM, 2017.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. 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Biedl, S. Huber, P. Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229.","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017.","apa":"Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195916600050","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229. doi:10.1142/S0218195916600050","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050.","ista":"Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229.","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Therese","full_name":"Biedl, Therese","last_name":"Biedl"},{"first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","last_name":"Huber","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814"},{"first_name":"Peter","full_name":"Palfrader, Peter","last_name":"Palfrader"}],"publist_id":"7338","title":"Planar matchings for weighted straight skeletons","acknowledgement":"Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.","oa":1,"quality_controlled":"1","publisher":"World Scientific Publishing","year":"2017","has_accepted_license":"1","publication":"International Journal of Computational Geometry and Applications","day":"13","page":"211 - 229","date_created":"2018-12-11T11:46:43Z","doi":"10.1142/S0218195916600050","date_published":"2017-04-13T00:00:00Z","_id":"481","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"949","status":"public","date_updated":"2023-02-21T16:06:22Z","ddc":["004","514","516"],"file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"HeEd"}],"abstract":[{"text":"We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 26","month":"04","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:09:34Z","file_name":"IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf","date_updated":"2020-07-14T12:46:35Z","file_size":769296,"creator":"system","file_id":"4758","checksum":"f79e8558bfe4b368dfefeb8eec2e3a5e","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"related_material":{"record":[{"id":"10892","status":"public","relation":"earlier_version"}]},"volume":26,"issue":"3-4"},{"date_updated":"2021-01-12T08:00:58Z","department":[{"_id":"RoSe"}],"_id":"484","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["10950761"]},"ec_funded":1,"issue":"3","volume":21,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory."}],"intvolume":" 21","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.04631"}],"scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.","apa":"Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4","ama":"Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4","short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738.","ieee":"P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017.","chicago":"Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4.","ista":"Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3), 683–738."},"title":"Bogoliubov correction to the mean-field dynamics of interacting bosons","author":[{"first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","full_name":"Nam, Phan"},{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7336","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication":"Advances in Theoretical and Mathematical Physics","day":"01","year":"2017","date_created":"2018-12-11T11:46:43Z","date_published":"2017-01-01T00:00:00Z","doi":"10.4310/ATMP.2017.v21.n3.a4","page":"683 - 738","oa":1,"publisher":"International Press","quality_controlled":"1"},{"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T08:00:57Z","status":"public","type":"journal_article","_id":"483","ec_funded":1,"volume":21,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["10950761"]},"intvolume":" 21","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1602.02312","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices.","lang":"eng"}],"title":"Universality for a class of random band matrices","author":[{"full_name":"Bourgade, Paul","last_name":"Bourgade","first_name":"Paul"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"full_name":"Yau, Horng","last_name":"Yau","first_name":"Horng"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"publist_id":"7337","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.","chicago":"Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5","ama":"Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800.","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017.","mla":"Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5."},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:46:43Z","doi":"10.4310/ATMP.2017.v21.n3.a5","date_published":"2017-08-25T00:00:00Z","page":"739 - 800","publication":"Advances in Theoretical and Mathematical Physics","day":"25","year":"2017","oa":1,"publisher":"International Press","quality_controlled":"1"},{"_id":"487","status":"public","type":"conference","conference":{"name":"CoNEXT: Conference on emerging Networking EXperiments and Technologies","start_date":"2017-12-12","location":"Incheon, South Korea","end_date":"2017-12-15"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.” Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367.","apa":"Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., & Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367","ama":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies. ACM; 2017:2-14. doi:10.1145/3143361.3143367","ieee":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L. Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies, Incheon, South Korea, 2017, pp. 2–14.","short":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu, in:, Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14.","chicago":"Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill, Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV White Spaces.” In Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367.","ista":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017. Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies. CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14."},"date_updated":"2023-02-23T12:21:11Z","department":[{"_id":"DaAl"}],"title":"Towards unlicensed cellular networks in TV white spaces","author":[{"first_name":"Ghufran","full_name":"Baig, Ghufran","last_name":"Baig"},{"full_name":"Radunovic, Bozidar","last_name":"Radunovic","first_name":"Bozidar"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Balkwill, Matthew","last_name":"Balkwill","first_name":"Matthew"},{"first_name":"Thomas","last_name":"Karagiannis","full_name":"Karagiannis, Thomas"},{"full_name":"Qiu, Lili","last_name":"Qiu","first_name":"Lili"}],"publist_id":"7333","oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x."}],"month":"11","scopus_import":1,"quality_controlled":"1","publisher":"ACM","day":"28","publication":"Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-145035422-6"]},"publication_status":"published","year":"2017","doi":"10.1145/3143361.3143367","date_published":"2017-11-28T00:00:00Z","date_created":"2018-12-11T11:46:45Z","page":"2 - 14"},{"title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","publist_id":"7305","author":[{"full_name":"Simonnet, Jean","last_name":"Simonnet","first_name":"Jean"},{"first_name":"Mérie","full_name":"Nassar, Mérie","last_name":"Nassar"},{"orcid":"0000-0001-9439-3148","full_name":"Stella, Federico","last_name":"Stella","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ivan","full_name":"Cohen, Ivan","last_name":"Cohen"},{"first_name":"Bertrand","full_name":"Mathon, Bertrand","last_name":"Mathon"},{"first_name":"Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte","last_name":"Boccara"},{"last_name":"Miles","full_name":"Miles, Richard","first_name":"Richard"},{"last_name":"Fricker","full_name":"Fricker, Desdemona","first_name":"Desdemona"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032","ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","ieee":"J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032.","ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032.","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032."},"article_number":"16032","date_published":"2017-07-01T00:00:00Z","doi":"10.1038/ncomms16032","date_created":"2018-12-11T11:46:54Z","day":"01","publication":"Nature Communications","has_accepted_license":"1","year":"2017","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:46:36Z","ddc":["571"],"date_updated":"2021-01-12T08:01:16Z","status":"public","pubrep_id":"937","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"514","volume":8,"file":[{"checksum":"76d8a2b72a58e56adb410ec37dfa7eee","file_id":"5083","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:14:31Z","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","creator":"system","date_updated":"2020-07-14T12:46:36Z","file_size":2948357}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","month":"07","intvolume":" 8","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.","lang":"eng"}]},{"type":"journal_article","article_type":"original","status":"public","_id":"515","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"LeSa"}],"date_updated":"2021-01-12T08:01:17Z","ddc":["572"],"scopus_import":1,"month":"10","intvolume":" 24","abstract":[{"text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.","lang":"eng"}],"oa_version":"Submitted Version","issue":"10","volume":24,"ec_funded":1,"publication_identifier":{"issn":["15459993"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6993","checksum":"9bc7e8c41b43636dd7566289e511f096","file_size":4118385,"date_updated":"2020-07-14T12:46:36Z","creator":"lsazanov","file_name":"29893_2_merged_1501257589_red.pdf","date_created":"2019-11-07T12:51:07Z"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"author":[{"last_name":"Letts","orcid":"0000-0002-9864-3586","full_name":"Letts, James A","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"publist_id":"7304","title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","citation":{"ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808.","ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460","apa":"Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460.","ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"page":"800 - 808","date_published":"2017-10-05T00:00:00Z","doi":"10.1038/nsmb.3460","date_created":"2018-12-11T11:46:54Z","has_accepted_license":"1","year":"2017","day":"05","publication":"Nature Structural and Molecular Biology"},{"month":"04","intvolume":" 2","quality_controlled":"1","scopus_import":1,"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.02619"}],"oa":1,"oa_version":"Preprint","abstract":[{"text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction.","lang":"eng"}],"issue":"4","date_published":"2017-04-01T00:00:00Z","volume":2,"doi":"10.1103/PhysRevFluids.2.043904","date_created":"2018-12-11T11:46:54Z","day":"01","publication":"Physical Review Fluids","language":[{"iso":"eng"}],"year":"2017","publication_status":"published","status":"public","type":"journal_article","article_number":"043904","_id":"513","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","department":[{"_id":"BjHo"}],"publist_id":"7306","author":[{"first_name":"Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1740-7635","full_name":"Klotz, Lukasz","last_name":"Klotz"},{"first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M","last_name":"Lemoult"},{"full_name":"Frontczak, Idalia","last_name":"Frontczak","first_name":"Idalia"},{"last_name":"Tuckerman","full_name":"Tuckerman, Laurette","first_name":"Laurette"},{"full_name":"Wesfreid, José","last_name":"Wesfreid","first_name":"José"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:16Z","citation":{"mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904","ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.","short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.","ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904."}},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["21615063"]},"issue":"3","volume":6,"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here."}],"intvolume":" 6","month":"03","scopus_import":1,"date_updated":"2021-01-12T08:01:21Z","department":[{"_id":"ToBo"}],"_id":"520","status":"public","type":"journal_article","article_type":"letter_note","publication":"ACS Synthetic Biology","day":"17","year":"2017","date_created":"2018-12-11T11:46:56Z","doi":"10.1021/acssynbio.6b00235","date_published":"2017-03-17T00:00:00Z","page":"395 - 401","quality_controlled":"1","publisher":"American Chemical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235.","ista":"Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401.","mla":"Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.","short":"W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.","ieee":"W. Du et al., “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” ACS Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017.","apa":"Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235","ama":"Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235"},"title":"Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803","external_id":{"pmid":["27936615"]},"author":[{"first_name":"Wei","full_name":"Du, Wei","last_name":"Du"},{"last_name":"Angermayr","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"full_name":"Jongbloets, Joeri","last_name":"Jongbloets","first_name":"Joeri"},{"first_name":"Douwe","full_name":"Molenaar, Douwe","last_name":"Molenaar"},{"first_name":"Herwig","full_name":"Bachmann, Herwig","last_name":"Bachmann"},{"first_name":"Klaas","full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf"},{"first_name":"Filipe","last_name":"Branco Dos Santos","full_name":"Branco Dos Santos, Filipe"}],"publist_id":"7298"},{"status":"public","type":"journal_article","_id":"521","department":[{"_id":"HeEd"}],"title":"Higson compactification and dimension raising","author":[{"last_name":"Austin","full_name":"Austin, Kyle","first_name":"Kyle"},{"first_name":"Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","full_name":"Virk, Ziga","last_name":"Virk"}],"publist_id":"7299","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:21Z","citation":{"chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.","ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.","apa":"Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005","ama":"Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005"},"intvolume":" 215","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1608.03954v1","open_access":"1"}],"oa":1,"publisher":"Elsevier","quality_controlled":"1","oa_version":"Submitted Version","abstract":[{"text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension.","lang":"eng"}],"date_created":"2018-12-11T11:46:56Z","volume":215,"date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.topol.2016.10.005","page":"45 - 57","language":[{"iso":"eng"}],"publication":"Topology and its Applications","day":"01","year":"2017","publication_status":"published","publication_identifier":{"issn":["01668641"]}},{"citation":{"ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0.","ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7283","author":[{"first_name":"Benjamin","last_name":"Burton","full_name":"Burton, Benjamin"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","first_name":"Arnaud N","full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1602.07907"]},"title":"Finding non-orientable surfaces in 3-Manifolds","year":"2017","day":"09","publication":"Discrete & Computational Geometry","page":"871 - 888","date_published":"2017-06-09T00:00:00Z","doi":"10.1007/s00454-017-9900-0","date_created":"2018-12-11T11:47:01Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2023-02-21T17:01:34Z","department":[{"_id":"UlWa"}],"_id":"534","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"issn":["01795376"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","related_material":{"record":[{"relation":"earlier_version","id":"1379","status":"public"}]},"volume":58,"abstract":[{"lang":"eng","text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.07907"}],"month":"06","intvolume":" 58"},{"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","file_id":"5007","creator":"system","date_updated":"2020-07-14T12:46:39Z","file_size":1668557,"date_created":"2018-12-12T10:13:24Z","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"16","volume":129,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"ger","text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. "}],"month":"05","intvolume":" 129","ddc":["571"],"date_updated":"2021-01-12T08:01:33Z","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:46:39Z","_id":"538","status":"public","pubrep_id":"932","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"20","publication":"Angewandte Chemie","has_accepted_license":"1","year":"2017","doi":"10.1002/ange.201611998","date_published":"2017-05-20T00:00:00Z","date_created":"2018-12-11T11:47:02Z","page":"4679 - 4682","publisher":"Wiley","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682."},"title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","author":[{"full_name":"Kainrath, Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"},{"first_name":"Manuela","full_name":"Stadler, Manuela","last_name":"Stadler"},{"last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"publist_id":"7279","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}]},{"article_number":"e1006758","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758"},"title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","publist_id":"7276","author":[{"first_name":"Kseniya","last_name":"Khamina","full_name":"Khamina, Kseniya"},{"last_name":"Lercher","full_name":"Lercher, Alexander","first_name":"Alexander"},{"first_name":"Michael","full_name":"Caldera, Michael","last_name":"Caldera"},{"first_name":"Christopher","full_name":"Schliehe, Christopher","last_name":"Schliehe"},{"first_name":"Bojan","full_name":"Vilagos, Bojan","last_name":"Vilagos"},{"last_name":"Sahin","full_name":"Sahin, Mehmet","first_name":"Mehmet"},{"last_name":"Kosack","full_name":"Kosack, Lindsay","first_name":"Lindsay"},{"full_name":"Bhattacharya, Anannya","last_name":"Bhattacharya","first_name":"Anannya"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"full_name":"Stukalov, Alexey","last_name":"Stukalov","first_name":"Alexey"},{"full_name":"Sacco, Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto"},{"first_name":"Leo","full_name":"James, Leo","last_name":"James"},{"full_name":"Pinschewer, Daniel","last_name":"Pinschewer","first_name":"Daniel"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"full_name":"Bergthaler, Andreas","last_name":"Bergthaler","first_name":"Andreas"}],"quality_controlled":"1","publisher":"Public Library of Science","oa":1,"day":"01","publication":"PLoS Pathogens","has_accepted_license":"1","year":"2017","doi":"10.1371/journal.ppat.1006758","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:47:03Z","_id":"540","status":"public","pubrep_id":"931","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576","616"],"date_updated":"2021-01-12T08:01:48Z","file_date_updated":"2020-07-14T12:46:44Z","department":[{"_id":"GaNo"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"month":"12","intvolume":" 13","scopus_import":1,"file":[{"file_id":"4944","checksum":"1aa20f19a1e90664fadce6e7d5284fdc","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","date_created":"2018-12-12T10:12:26Z","creator":"system","file_size":4106772,"date_updated":"2020-07-14T12:46:44Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15537366"]},"publication_status":"published","issue":"12","volume":13},{"publist_id":"7355","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Zuzana","last_name":"Křetínská","full_name":"Křetínská, Zuzana"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","citation":{"short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017).","ieee":"K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017","ama":"Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. 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International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"article_number":"15","date_created":"2018-12-11T11:46:38Z","date_published":"2017-07-03T00:00:00Z","doi":"10.23638/LMCS-13(2:15)2017","year":"2017","has_accepted_license":"1","publication":"Logical Methods in Computer Science","day":"03","oa":1,"quality_controlled":"1","publisher":"International Federation of Computational Logic","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:33Z","date_updated":"2023-02-23T12:26:16Z","ddc":["004"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"journal_article","pubrep_id":"957","status":"public","_id":"466","ec_funded":1,"volume":13,"related_material":{"record":[{"status":"public","id":"1657","relation":"earlier_version"},{"status":"public","id":"5429","relation":"earlier_version"},{"status":"public","id":"5435","relation":"earlier_version"}]},"issue":"2","publication_status":"published","publication_identifier":{"issn":["18605974"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:18:32Z","file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","creator":"system","date_updated":"2020-07-14T12:46:33Z","file_size":511832,"file_id":"5354","checksum":"bfa405385ec6229ad5ead89ab5751639","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":1,"intvolume":" 13","month":"07","abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. ","lang":"eng"}],"oa_version":"Published Version"},{"date_published":"2017-12-01T00:00:00Z","doi":"10.1145/3152769","date_created":"2018-12-11T11:46:38Z","day":"01","publication":"ACM Transactions on Computational Logic (TOCL)","year":"2017","publisher":"ACM","quality_controlled":"1","oa":1,"title":"Nested weighted automata","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7354","external_id":{"arxiv":["1606.03598"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017."},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"article_number":"31","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1656"},{"id":"5415","status":"public","relation":"earlier_version"},{"id":"5436","status":"public","relation":"earlier_version"}]},"issue":"4","volume":18,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15293785"]},"publication_status":"published","month":"12","intvolume":" 18","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1606.03598","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-02-23T12:26:19Z","status":"public","type":"journal_article","_id":"467"},{"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"1610","status":"public"},{"id":"5438","status":"public","relation":"earlier_version"}]},"volume":13,"issue":"3","publication_status":"published","publication_identifier":{"issn":["18605974"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:37Z","file_name":"IST-2015-321-v1+1_main.pdf","date_updated":"2020-07-14T12:46:33Z","file_size":279071,"creator":"system","file_id":"5090","checksum":"08041379ba408d40664f449eb5907a8f","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"08041379ba408d40664f449eb5907a8f","file_id":"5091","file_size":279071,"date_updated":"2020-07-14T12:46:33Z","creator":"system","file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","date_created":"2018-12-12T10:14:38Z"}],"scopus_import":1,"intvolume":" 13","month":"09","abstract":[{"text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:33Z","date_updated":"2023-02-23T12:26:25Z","ddc":["004"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"journal_article","pubrep_id":"955","status":"public","_id":"465","date_created":"2018-12-11T11:46:37Z","date_published":"2017-09-13T00:00:00Z","doi":"10.23638/LMCS-13(3:23)2017","year":"2017","has_accepted_license":"1","publication":"Logical Methods in Computer Science","day":"13","oa":1,"publisher":"International Federation of Computational Logic","quality_controlled":"1","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}],"publist_id":"7356","title":"Edit distance for pushdown automata","citation":{"mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017).","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"citation":{"short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 2017.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-00107-w","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"publist_id":"7307","title":"Amplification on undirected population structures: Comets beat stars","article_number":"82","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"year":"2017","has_accepted_license":"1","publication":"Scientific Reports","day":"06","date_created":"2018-12-11T11:46:53Z","date_published":"2017-03-06T00:00:00Z","doi":"10.1038/s41598-017-00107-w","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_updated":"2023-02-23T12:26:57Z","ddc":["004"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:36Z","_id":"512","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"938","status":"public","publication_status":"published","publication_identifier":{"issn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:18:35Z","file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","date_updated":"2020-07-14T12:46:36Z","file_size":1536783,"creator":"system","checksum":"7d05cbdd914e194a019c0f91fb64e9a8","file_id":"5357","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"ec_funded":1,"volume":7,"related_material":{"record":[{"relation":"earlier_version","id":"5449","status":"public"}]},"issue":"1","abstract":[{"lang":"eng","text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. 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