[{"author":[{"full_name":"Kügelgen, Julius von","first_name":"Julius von","last_name":"Kügelgen"},{"full_name":"Sharma, Yash","last_name":"Sharma","first_name":"Yash"},{"last_name":"Gresele","first_name":"Luigi","full_name":"Gresele, Luigi"},{"first_name":"Wieland","last_name":"Brendel","full_name":"Brendel, Wieland"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Besserve, Michel","first_name":"Michel","last_name":"Besserve"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"}],"extern":"1","day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Self-supervised learning with data augmentations provably isolates content from style","type":"conference","department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems","page":"16451-16467","date_created":"2023-08-22T14:04:36Z","quality_controlled":"1","volume":34,"external_id":{"arxiv":["2106.04619"]},"article_processing_charge":"No","_id":"14179","arxiv":1,"abstract":[{"lang":"eng","text":"Self-supervised representation learning has shown remarkable success in a number of domains. A common practice is to perform data augmentation via hand-crafted transformations intended to leave the semantics of the data invariant. We seek to understand the empirical success of this approach from a theoretical perspective. We formulate the augmentation process as a latent variable model by postulating a partition of the latent representation into a content component, which is assumed invariant to augmentation, and a style component, which is allowed to change. Unlike prior work on disentanglement and independent component analysis, we allow for both nontrivial statistical and causal dependencies in the latent space. We study the identifiability of the latent representation based on pairs of views of the observations and prove sufficient conditions that allow us to identify the invariant content partition up to an invertible mapping in both generative and discriminative settings. We find numerical simulations with dependent latent variables are consistent with our theory. Lastly, we introduce Causal3DIdent, a dataset of high-dimensional, visually complex images with rich causal dependencies, which we use to study the effect of data augmentations performed in practice."}],"date_updated":"2023-09-11T10:33:19Z","year":"2021","month":"06","status":"public","publication_identifier":{"isbn":["9781713845393"]},"oa":1,"oa_version":"Preprint","date_published":"2021-06-08T00:00:00Z","publication_status":"published","conference":{"start_date":"2021-12-07","name":"NeurIPS: Neural Information Processing Systems","end_date":"2021-12-10","location":"Virtual"},"citation":{"chicago":"Kügelgen, Julius von, Yash Sharma, Luigi Gresele, Wieland Brendel, Bernhard Schölkopf, Michel Besserve, and Francesco Locatello. “Self-Supervised Learning with Data Augmentations Provably Isolates Content from Style.” In <i>Advances in Neural Information Processing Systems</i>, 34:16451–67, 2021.","mla":"Kügelgen, Julius von, et al. “Self-Supervised Learning with Data Augmentations Provably Isolates Content from Style.” <i>Advances in Neural Information Processing Systems</i>, vol. 34, 2021, pp. 16451–67.","apa":"Kügelgen, J. von, Sharma, Y., Gresele, L., Brendel, W., Schölkopf, B., Besserve, M., &#38; Locatello, F. (2021). Self-supervised learning with data augmentations provably isolates content from style. In <i>Advances in Neural Information Processing Systems</i> (Vol. 34, pp. 16451–16467). Virtual.","ista":"Kügelgen J von, Sharma Y, Gresele L, Brendel W, Schölkopf B, Besserve M, Locatello F. 2021. Self-supervised learning with data augmentations provably isolates content from style. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 16451–16467.","ieee":"J. von Kügelgen <i>et al.</i>, “Self-supervised learning with data augmentations provably isolates content from style,” in <i>Advances in Neural Information Processing Systems</i>, Virtual, 2021, vol. 34, pp. 16451–16467.","ama":"Kügelgen J von, Sharma Y, Gresele L, et al. Self-supervised learning with data augmentations provably isolates content from style. In: <i>Advances in Neural Information Processing Systems</i>. Vol 34. ; 2021:16451-16467.","short":"J. von Kügelgen, Y. Sharma, L. Gresele, W. Brendel, B. Schölkopf, M. Besserve, F. Locatello, in:, Advances in Neural Information Processing Systems, 2021, pp. 16451–16467."},"intvolume":"        34","main_file_link":[{"url":"https://arxiv.org/abs/2106.04619","open_access":"1"}]},{"author":[{"first_name":"Nasim","last_name":"Rahaman","full_name":"Rahaman, Nasim"},{"full_name":"Gondal, Muhammad Waleed","first_name":"Muhammad Waleed","last_name":"Gondal"},{"last_name":"Joshi","first_name":"Shruti","full_name":"Joshi, Shruti"},{"first_name":"Peter","last_name":"Gehler","full_name":"Gehler, Peter"},{"full_name":"Bengio, Yoshua","first_name":"Yoshua","last_name":"Bengio"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"}],"day":"12","extern":"1","title":"Dynamic inference with neural interpreters","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"type":"conference","page":"10985-10998","date_created":"2023-08-22T14:04:55Z","publication":"Advances in Neural Information Processing Systems","external_id":{"arxiv":["2110.06399"]},"volume":34,"quality_controlled":"1","article_processing_charge":"No","_id":"14180","year":"2021","date_updated":"2023-09-11T11:33:46Z","abstract":[{"text":"Modern neural network architectures can leverage large amounts of data to generalize well within the training distribution. However, they are less capable of systematic generalization to data drawn from unseen but related distributions, a feat that is hypothesized to require compositional reasoning and reuse of knowledge. In this work, we present Neural Interpreters, an architecture that factorizes inference in a self-attention network as a system of modules, which we call \\emph{functions}. Inputs to the model are routed through a sequence of functions in a way that is end-to-end learned. The proposed architecture can flexibly compose computation along width and depth, and lends itself well to capacity extension after training. To demonstrate the versatility of Neural Interpreters, we evaluate it in two distinct settings: image classification and visual abstract reasoning on Raven Progressive Matrices. In the former, we show that Neural Interpreters perform on par with the vision transformer using fewer parameters, while being transferrable to a new task in a sample efficient manner. In the latter, we find that Neural Interpreters are competitive with respect to the state-of-the-art in terms of systematic generalization. ","lang":"eng"}],"arxiv":1,"month":"10","publication_identifier":{"isbn":["9781713845393"]},"oa":1,"status":"public","date_published":"2021-10-12T00:00:00Z","oa_version":"Preprint","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2021-12-07","location":"Virtual","end_date":"2021-12-10"},"publication_status":"published","intvolume":"        34","citation":{"short":"N. Rahaman, M.W. Gondal, S. Joshi, P. Gehler, Y. Bengio, F. Locatello, B. Schölkopf, in:, Advances in Neural Information Processing Systems, 2021, pp. 10985–10998.","ieee":"N. Rahaman <i>et al.</i>, “Dynamic inference with neural interpreters,” in <i>Advances in Neural Information Processing Systems</i>, Virtual, 2021, vol. 34, pp. 10985–10998.","ama":"Rahaman N, Gondal MW, Joshi S, et al. Dynamic inference with neural interpreters. In: <i>Advances in Neural Information Processing Systems</i>. Vol 34. ; 2021:10985-10998.","chicago":"Rahaman, Nasim, Muhammad Waleed Gondal, Shruti Joshi, Peter Gehler, Yoshua Bengio, Francesco Locatello, and Bernhard Schölkopf. “Dynamic Inference with Neural Interpreters.” In <i>Advances in Neural Information Processing Systems</i>, 34:10985–98, 2021.","mla":"Rahaman, Nasim, et al. “Dynamic Inference with Neural Interpreters.” <i>Advances in Neural Information Processing Systems</i>, vol. 34, 2021, pp. 10985–98.","apa":"Rahaman, N., Gondal, M. W., Joshi, S., Gehler, P., Bengio, Y., Locatello, F., &#38; Schölkopf, B. (2021). Dynamic inference with neural interpreters. In <i>Advances in Neural Information Processing Systems</i> (Vol. 34, pp. 10985–10998). Virtual.","ista":"Rahaman N, Gondal MW, Joshi S, Gehler P, Bengio Y, Locatello F, Schölkopf B. 2021. Dynamic inference with neural interpreters. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 10985–10998."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2110.06399"}]},{"_id":"14181","date_updated":"2023-09-11T11:14:30Z","arxiv":1,"abstract":[{"text":"Variational Inference makes a trade-off between the capacity of the variational family and the tractability of finding an approximate posterior distribution. Instead, Boosting Variational Inference allows practitioners to obtain increasingly good posterior approximations by spending more compute. The main obstacle to widespread adoption of Boosting Variational Inference is the amount of resources necessary to improve over a strong Variational Inference baseline. In our work, we trace this limitation back to the global curvature of the KL-divergence. We characterize how the global curvature impacts time and memory consumption, address the problem with the notion of local curvature, and provide a novel approximate backtracking algorithm for estimating local curvature. We give new theoretical convergence rates for our algorithms and provide experimental validation on synthetic and real-world datasets.","lang":"eng"}],"year":"2021","month":"05","status":"public","oa":1,"publication_identifier":{"eisbn":["9780999241196"]},"oa_version":"Published Version","date_published":"2021-05-19T00:00:00Z","conference":{"location":"Montreal, Canada","end_date":"2021-08-27","name":"IJCAI: International Joint Conference on Artificial Intelligence","start_date":"2021-08-19"},"publication_status":"published","doi":"10.24963/ijcai.2021/322","citation":{"apa":"Dresdner, G., Shekhar, S., Pedregosa, F., Locatello, F., &#38; Rätsch, G. (2021). Boosting variational inference with locally adaptive step-sizes. In <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i> (pp. 2337–2343). Montreal, Canada: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2021/322\">https://doi.org/10.24963/ijcai.2021/322</a>","mla":"Dresdner, Gideon, et al. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–43, doi:<a href=\"https://doi.org/10.24963/ijcai.2021/322\">10.24963/ijcai.2021/322</a>.","ista":"Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. 2021. Boosting variational inference with locally adaptive step-sizes. Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 2337–2343.","chicago":"Dresdner, Gideon, Saurav Shekhar, Fabian Pedregosa, Francesco Locatello, and Gunnar Rätsch. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” In <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>, 2337–43. International Joint Conferences on Artificial Intelligence, 2021. <a href=\"https://doi.org/10.24963/ijcai.2021/322\">https://doi.org/10.24963/ijcai.2021/322</a>.","ieee":"G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, and G. Rätsch, “Boosting variational inference with locally adaptive step-sizes,” in <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>, Montreal, Canada, 2021, pp. 2337–2343.","ama":"Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. Boosting variational inference with locally adaptive step-sizes. In: <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2021:2337-2343. doi:<a href=\"https://doi.org/10.24963/ijcai.2021/322\">10.24963/ijcai.2021/322</a>","short":"G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, G. Rätsch, in:, Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–2343."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.09240"}],"author":[{"last_name":"Dresdner","first_name":"Gideon","full_name":"Dresdner, Gideon"},{"first_name":"Saurav","last_name":"Shekhar","full_name":"Shekhar, Saurav"},{"first_name":"Fabian","last_name":"Pedregosa","full_name":"Pedregosa, Fabian"},{"first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"}],"day":"19","extern":"1","publisher":"International Joint Conferences on Artificial Intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Boosting variational inference with locally adaptive step-sizes","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"page":"2337-2343","date_created":"2023-08-22T14:05:14Z","publication":"Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence","external_id":{"arxiv":["2105.09240"]},"quality_controlled":"1","article_processing_charge":"No"},{"page":"116-128","date_created":"2023-08-22T14:05:41Z","publication":"35th Conference on Neural Information Processing Systems","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"article_processing_charge":"No","external_id":{"arxiv":["2107.01057"]},"volume":34,"quality_controlled":"1","day":"02","extern":"1","author":[{"first_name":"Frederik","last_name":"Träuble","full_name":"Träuble, Frederik"},{"first_name":"Julius von","last_name":"Kügelgen","full_name":"Kügelgen, Julius von"},{"first_name":"Matthäus","last_name":"Kleindessner","full_name":"Kleindessner, Matthäus"},{"full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Gehler, Peter","last_name":"Gehler","first_name":"Peter"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Backward-compatible prediction updates: A probabilistic approach","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2021-12-07","location":"Virtual","end_date":"2021-12-10"},"publication_status":"published","oa_version":"Preprint","date_published":"2021-07-02T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.01057"}],"citation":{"chicago":"Träuble, Frederik, Julius von Kügelgen, Matthäus Kleindessner, Francesco Locatello, Bernhard Schölkopf, and Peter Gehler. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:116–28, 2021.","apa":"Träuble, F., Kügelgen, J. von, Kleindessner, M., Locatello, F., Schölkopf, B., &#38; Gehler, P. (2021). Backward-compatible prediction updates: A probabilistic approach. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 116–128). Virtual.","mla":"Träuble, Frederik, et al. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, 2021, pp. 116–28.","ista":"Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. 2021. Backward-compatible prediction updates: A probabilistic approach. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 116–128.","short":"F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, P. Gehler, in:, 35th Conference on Neural Information Processing Systems, 2021, pp. 116–128.","ama":"Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. Backward-compatible prediction updates: A probabilistic approach. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. ; 2021:116-128.","ieee":"F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, and P. Gehler, “Backward-compatible prediction updates: A probabilistic approach,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, 2021, vol. 34, pp. 116–128."},"intvolume":"        34","date_updated":"2023-09-11T11:31:59Z","arxiv":1,"abstract":[{"text":"When machine learning systems meet real world applications, accuracy is only\r\none of several requirements. In this paper, we assay a complementary\r\nperspective originating from the increasing availability of pre-trained and\r\nregularly improving state-of-the-art models. While new improved models develop\r\nat a fast pace, downstream tasks vary more slowly or stay constant. Assume that\r\nwe have a large unlabelled data set for which we want to maintain accurate\r\npredictions. Whenever a new and presumably better ML models becomes available,\r\nwe encounter two problems: (i) given a limited budget, which data points should\r\nbe re-evaluated using the new model?; and (ii) if the new predictions differ\r\nfrom the current ones, should we update? Problem (i) is about compute cost,\r\nwhich matters for very large data sets and models. Problem (ii) is about\r\nmaintaining consistency of the predictions, which can be highly relevant for\r\ndownstream applications; our demand is to avoid negative flips, i.e., changing\r\ncorrect to incorrect predictions. In this paper, we formalize the Prediction\r\nUpdate Problem and present an efficient probabilistic approach as answer to the\r\nabove questions. In extensive experiments on standard classification benchmark\r\ndata sets, we show that our method outperforms alternative strategies along key\r\nmetrics for backward-compatible prediction updates.","lang":"eng"}],"year":"2021","_id":"14182","status":"public","oa":1,"publication_identifier":{"isbn":["9781713845393"]},"month":"07"},{"citation":{"chicago":"Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2111.13693\">https://doi.org/10.48550/arXiv.2111.13693</a>.","mla":"Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.” <i>ArXiv</i>, 2111.13693, doi:<a href=\"https://doi.org/10.48550/arXiv.2111.13693\">10.48550/arXiv.2111.13693</a>.","apa":"Locatello, F. (n.d.). Enforcing and discovering structure in machine learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2111.13693\">https://doi.org/10.48550/arXiv.2111.13693</a>","ista":"Locatello F. Enforcing and discovering structure in machine learning. arXiv, 2111.13693.","ama":"Locatello F. Enforcing and discovering structure in machine learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2111.13693\">10.48550/arXiv.2111.13693</a>","ieee":"F. Locatello, “Enforcing and discovering structure in machine learning,” <i>arXiv</i>. .","short":"F. Locatello, ArXiv (n.d.)."},"external_id":{"arxiv":["2111.13693"]},"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.13693","open_access":"1"}],"date_published":"2021-11-26T00:00:00Z","department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"type":"preprint","oa_version":"Preprint","publication":"arXiv","date_created":"2023-08-22T14:23:35Z","doi":"10.48550/arXiv.2111.13693","publication_status":"submitted","month":"11","oa":1,"title":"Enforcing and discovering structure in machine learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"14221","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"}],"article_number":"2111.13693","extern":"1","year":"2021","day":"26","abstract":[{"lang":"eng","text":"The world is structured in countless ways. It may be prudent to enforce corresponding structural properties to a learning algorithm's solution, such as incorporating prior beliefs, natural constraints, or causal structures. Doing so may translate to faster, more accurate, and more flexible models, which may directly relate to real-world impact. In this dissertation, we consider two different research areas that concern structuring a learning algorithm's solution: when the structure is known and when it has to be discovered."}],"arxiv":1,"date_updated":"2023-09-12T07:04:44Z"},{"intvolume":"        67","citation":{"ieee":"A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with optimal scaling: Polar codes with large kernels,” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.","ama":"Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. 2021;67(9):5693-5710. doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>","short":"A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information Theory 67 (2021) 5693–5710.","chicago":"Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>.","apa":"Fazeli, A., Hassani, H., Mondelli, M., &#38; Vardy, A. (2021). Binary linear codes with optimal scaling: Polar codes with large kernels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2020.3038806\">https://doi.org/10.1109/TIT.2020.3038806</a>","mla":"Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” <i>IEEE Transactions on Information Theory</i>, vol. 67, no. 9, IEEE, 2021, pp. 5693–710, doi:<a href=\"https://doi.org/10.1109/TIT.2020.3038806\">10.1109/TIT.2020.3038806</a>.","ista":"Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with optimal scaling: Polar codes with large kernels. IEEE Transactions on Information Theory. 67(9), 5693–5710."},"scopus_import":"1","oa_version":"Preprint","date_published":"2021-09-01T00:00:00Z","doi":"10.1109/TIT.2020.3038806","publication_status":"published","month":"09","status":"public","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"_id":"9002","arxiv":1,"issue":"9","abstract":[{"lang":"eng","text":" We prove that, for the binary erasure channel (BEC), the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Our proof is based on the construction and analysis of binary polar codes with large kernels. When communicating reliably at rates within ε>0 of capacity, the code length n often scales as O(1/εμ), where the constant μ is called the scaling exponent. It is known that the optimal scaling exponent is μ=2, and it is achieved by random linear codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel) on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by random codes. Our main contribution is a rigorous proof of the following result: for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain the recursive structure of conventional polar codes, and thereby achieve construction complexity O(n) and encoding/decoding complexity O(nlogn)."}],"date_updated":"2024-03-07T12:18:50Z","year":"2021","quality_controlled":"1","volume":67,"external_id":{"arxiv":["1711.01339"]},"related_material":{"record":[{"id":"6665","relation":"earlier_version","status":"public"}]},"article_processing_charge":"No","article_type":"original","type":"journal_article","department":[{"_id":"MaMo"}],"language":[{"iso":"eng"}],"publication":"IEEE Transactions on Information Theory","date_created":"2021-01-10T23:01:18Z","page":"5693-5710","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","title":"Binary linear codes with optimal scaling: Polar codes with large kernels","author":[{"first_name":"Arman","last_name":"Fazeli","full_name":"Fazeli, Arman"},{"first_name":"Hamed","last_name":"Hassani","full_name":"Hassani, Hamed"},{"full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"full_name":"Vardy, Alexander","first_name":"Alexander","last_name":"Vardy"}],"day":"01"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.05948"}],"intvolume":"       126","citation":{"short":"M. Brooks, M. Lemeshko, D. Lundholm, E. Yakaboylu, Physical Review Letters 126 (2021).","ama":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. Molecular impurities as a realization of anyons on the two-sphere. <i>Physical Review Letters</i>. 2021;126(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">10.1103/PhysRevLett.126.015301</a>","ieee":"M. Brooks, M. Lemeshko, D. Lundholm, and E. Yakaboylu, “Molecular impurities as a realization of anyons on the two-sphere,” <i>Physical Review Letters</i>, vol. 126, no. 1. American Physical Society, 2021.","chicago":"Brooks, Morris, Mikhail Lemeshko, D. Lundholm, and Enderalp Yakaboylu. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">https://doi.org/10.1103/PhysRevLett.126.015301</a>.","ista":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. 2021. Molecular impurities as a realization of anyons on the two-sphere. Physical Review Letters. 126(1), 015301.","apa":"Brooks, M., Lemeshko, M., Lundholm, D., &#38; Yakaboylu, E. (2021). Molecular impurities as a realization of anyons on the two-sphere. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">https://doi.org/10.1103/PhysRevLett.126.015301</a>","mla":"Brooks, Morris, et al. “Molecular Impurities as a Realization of Anyons on the Two-Sphere.” <i>Physical Review Letters</i>, vol. 126, no. 1, 015301, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.015301\">10.1103/PhysRevLett.126.015301</a>."},"doi":"10.1103/PhysRevLett.126.015301","publication_status":"published","date_published":"2021-01-08T00:00:00Z","oa_version":"Preprint","oa":1,"publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"status":"public","ec_funded":1,"month":"01","year":"2021","arxiv":1,"abstract":[{"lang":"eng","text":"Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field."}],"issue":"1","date_updated":"2023-08-07T13:32:10Z","_id":"9005","article_number":"015301","article_processing_charge":"No","article_type":"original","related_material":{"link":[{"url":"https://ist.ac.at/en/news/dancing-molecules-and-two-dimensional-particles/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"12390","relation":"dissertation_contains","status":"public"}]},"quality_controlled":"1","volume":126,"external_id":{"arxiv":["2009.05948"],"isi":["000606325000003"]},"publication":"Physical Review Letters","date_created":"2021-01-17T23:01:10Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"Molecular impurities as a realization of anyons on the two-sphere","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","day":"08","acknowledgement":"We are grateful to A. Ghazaryan for valuable discussions and also thank the anonymous referees for comments. D.L. acknowledges financial support from the G¨oran Gustafsson Foundation (grant no. 1804) and LMU Munich. M.L. gratefully acknowledges financial support\r\nby the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 801770).","author":[{"full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928","first_name":"Morris","last_name":"Brooks","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"first_name":"D.","last_name":"Lundholm","full_name":"Lundholm, D."},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp"}],"isi":1,"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}]},{"author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"},{"full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"isi":1,"day":"25","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","pmid":1,"title":"Cytoplasm's got moves","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Developmental Cell","page":"P213-226","date_created":"2021-01-17T23:01:10Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9623"}]},"volume":56,"quality_controlled":"1","external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"article_processing_charge":"No","article_type":"original","_id":"9006","year":"2021","issue":"2","abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species."}],"date_updated":"2024-03-25T23:30:10Z","month":"01","oa":1,"publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"status":"public","date_published":"2021-01-25T00:00:00Z","oa_version":"Published Version","doi":"10.1016/j.devcel.2020.12.002","publication_status":"published","citation":{"mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>.","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","apa":"Shamipour, S., Caballero Mancebo, S., &#38; Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>.","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” <i>Developmental Cell</i>, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. <i>Developmental Cell</i>. 2021;56(2):P213-226. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226."},"intvolume":"        56","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"scopus_import":"1"},{"month":"02","status":"public","oa":1,"publication_identifier":{"issn":["1360-8185"],"eissn":["1573-675X"]},"_id":"9009","issue":"2","abstract":[{"lang":"eng","text":"Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane."}],"date_updated":"2023-08-07T13:32:40Z","year":"2021","intvolume":"        26","citation":{"mla":"Grosser, Joshua A., et al. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>, vol. 26, no. 2, Springer Nature, 2021, pp. 132–45, doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>.","ista":"Grosser JA, Maes ME, Nickells RW. 2021. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. Apoptosis. 26(2), 132–145.","apa":"Grosser, J. A., Maes, M. E., &#38; Nickells, R. W. (2021). Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>","chicago":"Grosser, Joshua A., Margaret E Maes, and Robert W. Nickells. “Characteristics of Intracellular Propagation of Mitochondrial BAX Recruitment during Apoptosis.” <i>Apoptosis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s10495-020-01654-w\">https://doi.org/10.1007/s10495-020-01654-w</a>.","short":"J.A. Grosser, M.E. Maes, R.W. Nickells, Apoptosis 26 (2021) 132–145.","ama":"Grosser JA, Maes ME, Nickells RW. Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis. <i>Apoptosis</i>. 2021;26(2):132-145. doi:<a href=\"https://doi.org/10.1007/s10495-020-01654-w\">10.1007/s10495-020-01654-w</a>","ieee":"J. A. Grosser, M. E. Maes, and R. W. Nickells, “Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis,” <i>Apoptosis</i>, vol. 26, no. 2. Springer Nature, pp. 132–145, 2021."},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082518/"}],"oa_version":"Submitted Version","date_published":"2021-02-01T00:00:00Z","doi":"10.1007/s10495-020-01654-w","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis","isi":1,"author":[{"full_name":"Grosser, Joshua A.","first_name":"Joshua A.","last_name":"Grosser"},{"full_name":"Maes, Margaret E","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085"},{"full_name":"Nickells, Robert W.","first_name":"Robert W.","last_name":"Nickells"}],"pmid":1,"acknowledgement":"This work was supported by National Institute of Health grants R01 EY030123, P30 EY016665, and T32 GM081061, an unrestricted research grant from Research to Prevent Blindness, Inc., and the Frederick A. Davis Endowment from the Department of Ophthalmology and Visual Sciences at the University of Wisconsin-Madison.","day":"01","volume":26,"quality_controlled":"1","external_id":{"pmid":["33426618"],"isi":["000606722600001"]},"article_processing_charge":"No","article_type":"original","type":"journal_article","department":[{"_id":"SaSi"}],"language":[{"iso":"eng"}],"publication":"Apoptosis","date_created":"2021-01-17T23:01:11Z","page":"132-145"},{"project":[{"call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16"},{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"isi":1,"author":[{"full_name":"Ötvös, Krisztina","first_name":"Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marconi, Marco","first_name":"Marco","last_name":"Marconi"},{"last_name":"Vega","first_name":"Andrea","full_name":"Vega, Andrea"},{"last_name":"O’Brien","first_name":"Jose","full_name":"O’Brien, Jose"},{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"full_name":"Abualia, Rashed","first_name":"Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Antonielli","first_name":"Livio","full_name":"Antonielli, Livio"},{"orcid":"0000-0001-9179-6099","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","full_name":"Montesinos López, Juan C"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang"},{"last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","full_name":"Tan, Shutang"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","first_name":"Candela","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela"},{"full_name":"Artner, Christina","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner"},{"full_name":"Bouguyon, Eleonore","first_name":"Eleonore","last_name":"Bouguyon"},{"first_name":"Alain","last_name":"Gojon","full_name":"Gojon, Alain"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."},{"full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"file":[{"access_level":"open_access","creator":"dernst","file_id":"9110","checksum":"dc55c900f3b061d6c2790b8813d759a3","date_created":"2021-02-11T12:28:29Z","file_name":"2021_Embo_Otvos.pdf","date_updated":"2021-02-11T12:28:29Z","file_size":2358617,"success":1,"relation":"main_file","content_type":"application/pdf"}],"acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","pmid":1,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by/4.0/","publisher":"Embo Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"has_accepted_license":"1","date_created":"2021-01-17T23:01:12Z","publication":"EMBO Journal","external_id":{"pmid":[" 33399250"],"isi":["000604645600001"]},"volume":40,"quality_controlled":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/"}]},"article_processing_charge":"Yes (via OA deal)","article_type":"original","article_number":"e106862","acknowledged_ssus":[{"_id":"Bio"}],"_id":"9010","date_updated":"2024-03-25T23:30:22Z","issue":"3","abstract":[{"lang":"eng","text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments."}],"year":"2021","month":"02","status":"public","oa":1,"publication_identifier":{"issn":["02614189"],"eissn":["14602075"]},"oa_version":"Published Version","date_published":"2021-02-01T00:00:00Z","publication_status":"published","doi":"10.15252/embj.2020106862","citation":{"short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 2021.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>.","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>."},"intvolume":"        40","scopus_import":"1","file_date_updated":"2021-02-11T12:28:29Z","ddc":["580"]},{"doi":"10.3390/e23010125","publication_status":"published","date_published":"2021-01-19T00:00:00Z","oa_version":"Published Version","ddc":["530"],"file_date_updated":"2021-01-19T11:11:14Z","citation":{"short":"T. Gulden, A. Kamenev, Entropy 23 (2021).","ieee":"T. Gulden and A. Kamenev, “Dynamics of ion channels via non-hermitian quantum mechanics,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","ama":"Gulden T, Kamenev A. Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>","chicago":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>.","mla":"Gulden, Tobias, and Alex Kamenev. “Dynamics of Ion Channels via Non-Hermitian Quantum Mechanics.” <i>Entropy</i>, vol. 23, no. 1, e23010125, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010125\">10.3390/e23010125</a>.","ista":"Gulden T, Kamenev A. 2021. Dynamics of ion channels via non-hermitian quantum mechanics. Entropy. 23(1), e23010125.","apa":"Gulden, T., &#38; Kamenev, A. (2021). Dynamics of ion channels via non-hermitian quantum mechanics. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010125\">https://doi.org/10.3390/e23010125</a>"},"intvolume":"        23","year":"2021","arxiv":1,"abstract":[{"lang":"eng","text":"We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. "}],"issue":"1","date_updated":"2023-08-07T13:34:18Z","_id":"9020","article_number":"e23010125","publication_identifier":{"eissn":["1099-4300"]},"oa":1,"status":"public","ec_funded":1,"month":"01","publication":"Entropy","date_created":"2021-01-19T11:12:06Z","has_accepted_license":"1","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"Yes","article_type":"original","quality_controlled":"1","volume":23,"external_id":{"isi":["000610122000001"],"arxiv":["2012.01390"]},"day":"19","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"A.K. was supported by NSF grants DMR-2037654. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nWe are indebted to Boris Shklovskii for introducing us to the problem, and Alexander Gorsky and Peter Koroteev for introducing us to the Picard-Fuchs methods. A very special thanks goes to Michael Janas for several years of excellent collaboration on these topics. TG thanks Michael Kreshchuk for introduction to the exact WKB method and great collaboration on related projects. Figure 3 and Figure 4 are reproduced from Reference [25] with friendly permission by the Russian Academy of Sciences. Figure 2, Figure 4, Figure 5, Figure 6, and Figure 8 are reproduced from Reference [26] with friendly permission by IOP Publishing.","file":[{"checksum":"6cd0e706156827c45c740534bd32c179","creator":"tgulden","file_id":"9021","access_level":"open_access","file_name":"Final published paper.pdf","date_updated":"2021-01-19T11:11:14Z","date_created":"2021-01-19T11:11:14Z","content_type":"application/pdf","relation":"main_file","file_size":981285}],"author":[{"full_name":"Gulden, Tobias","first_name":"Tobias","orcid":"0000-0001-6814-7541","last_name":"Gulden","id":"1083E038-9F73-11E9-A4B5-532AE6697425"},{"first_name":"Alex","last_name":"Kamenev","full_name":"Kamenev, Alex"}],"isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"title":"Dynamics of ion channels via non-hermitian quantum mechanics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"MDPI"},{"ec_funded":1,"month":"01","oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","_id":"9022","year":"2021","abstract":[{"text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.","lang":"eng"}],"date_updated":"2023-09-07T13:29:32Z","citation":{"ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>.","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","apa":"Cipolloni, G. (2021). <i>Fluctuations in the spectrum of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9022\">https://doi.org/10.15479/AT:ISTA:9022</a>","mla":"Cipolloni, Giorgio. <i>Fluctuations in the Spectrum of Random Matrices</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9022\">10.15479/AT:ISTA:9022</a>."},"ddc":["510"],"file_date_updated":"2021-01-25T14:19:10Z","date_published":"2021-01-25T00:00:00Z","oa_version":"Published Version","doi":"10.15479/AT:ISTA:9022","publication_status":"published","supervisor":[{"full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603"}],"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"title":"Fluctuations in the spectrum of random matrices","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/pdf","relation":"main_file","file_size":4127796,"success":1,"file_name":"thesis.pdf","date_updated":"2021-01-25T14:19:03Z","date_created":"2021-01-25T14:19:03Z","creator":"gcipollo","file_id":"9043","checksum":"5a93658a5f19478372523ee232887e2b","access_level":"open_access"},{"content_type":"application/zip","relation":"source_file","file_size":12775206,"checksum":"e8270eddfe6a988e92a53c88d1d19b8c","creator":"gcipollo","file_id":"9044","access_level":"closed","file_name":"Thesis_files.zip","date_updated":"2021-01-25T14:19:10Z","date_created":"2021-01-25T14:19:10Z"}],"author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"day":"25","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"language":[{"iso":"eng"}],"type":"dissertation","date_created":"2021-01-21T18:16:54Z","page":"380","has_accepted_license":"1"},{"acknowledgement":"D. Virosztek was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","day":"26","author":[{"full_name":"Virosztek, Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","first_name":"Daniel"}],"isi":1,"project":[{"grant_number":"846294","_id":"26A455A6-B435-11E9-9278-68D0E5697425","name":"Geometric study of Wasserstein spaces and free probability","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","title":"The metric property of the quantum Jensen-Shannon divergence","publication":"Advances in Mathematics","date_created":"2021-01-22T17:55:17Z","type":"journal_article","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","keyword":["General Mathematics"],"volume":380,"quality_controlled":"1","external_id":{"isi":["000619676100035"],"arxiv":["1910.10447"]},"issue":"3","arxiv":1,"abstract":[{"lang":"eng","text":"In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space."}],"date_updated":"2023-08-07T13:34:48Z","year":"2021","article_number":"107595","_id":"9036","status":"public","publication_identifier":{"issn":["0001-8708"]},"oa":1,"month":"03","ec_funded":1,"doi":"10.1016/j.aim.2021.107595","publication_status":"published","oa_version":"Preprint","date_published":"2021-03-26T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10447"}],"intvolume":"       380","citation":{"ama":"Virosztek D. The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. 2021;380(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>","ieee":"D. Virosztek, “The metric property of the quantum Jensen-Shannon divergence,” <i>Advances in Mathematics</i>, vol. 380, no. 3. Elsevier, 2021.","short":"D. Virosztek, Advances in Mathematics 380 (2021).","chicago":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>.","mla":"Virosztek, Daniel. “The Metric Property of the Quantum Jensen-Shannon Divergence.” <i>Advances in Mathematics</i>, vol. 380, no. 3, 107595, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107595\">10.1016/j.aim.2021.107595</a>.","ista":"Virosztek D. 2021. The metric property of the quantum Jensen-Shannon divergence. Advances in Mathematics. 380(3), 107595.","apa":"Virosztek, D. (2021). The metric property of the quantum Jensen-Shannon divergence. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2021.107595\">https://doi.org/10.1016/j.aim.2021.107595</a>"}},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"London Mathematical Society","file":[{"success":1,"file_size":194550,"content_type":"application/pdf","relation":"main_file","date_created":"2021-08-06T09:59:45Z","file_name":"2021_BLMS_Ivanov.pdf","date_updated":"2021-08-06T09:59:45Z","access_level":"open_access","file_id":"9796","creator":"kschuh","checksum":"e6ceaa6470d835eb4c211cbdd38fdfd1"}],"isi":1,"author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"}],"day":"01","tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"I wish to thank Imre Bárány for bringing the problem to my attention. I am grateful to Marton Naszódi and Igor Tsiutsiurupa for useful remarks and help with the text.\r\nThe author acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075‐15‐2019‐1926.","volume":53,"quality_controlled":"1","external_id":{"arxiv":["1912.08561"],"isi":["000607265100001"]},"article_processing_charge":"Yes (via OA deal)","article_type":"original","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Bulletin of the London Mathematical Society","page":"631-641","date_created":"2021-01-24T23:01:08Z","has_accepted_license":"1","month":"04","publication_identifier":{"eissn":["14692120"],"issn":["00246093"]},"oa":1,"status":"public","_id":"9037","year":"2021","issue":"2","abstract":[{"text":"We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak  𝜀 ‐net theorem in Banach spaces of type  𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma.","lang":"eng"}],"arxiv":1,"date_updated":"2023-08-07T13:35:20Z","citation":{"ieee":"G. Ivanov, “No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. London Mathematical Society, pp. 631–641, 2021.","ama":"Ivanov G. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):631-641. doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>","short":"G. Ivanov, Bulletin of the London Mathematical Society 53 (2021) 631–641.","chicago":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society, 2021. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>.","ista":"Ivanov G. 2021. No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. Bulletin of the London Mathematical Society. 53(2), 631–641.","apa":"Ivanov, G. (2021). No-dimension Tverberg’s theorem and its corollaries in Banach spaces of type p. <i>Bulletin of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/blms.12449\">https://doi.org/10.1112/blms.12449</a>","mla":"Ivanov, Grigory. “No-Dimension Tverberg’s Theorem and Its Corollaries in Banach Spaces of Type P.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, London Mathematical Society, 2021, pp. 631–41, doi:<a href=\"https://doi.org/10.1112/blms.12449\">10.1112/blms.12449</a>."},"intvolume":"        53","ddc":["510"],"scopus_import":"1","file_date_updated":"2021-08-06T09:59:45Z","date_published":"2021-04-01T00:00:00Z","oa_version":"Published Version","doi":"10.1112/blms.12449","publication_status":"published"},{"ddc":["570"],"scopus_import":"1","file_date_updated":"2021-02-03T12:13:03Z","intvolume":"        17","citation":{"chicago":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>.","mla":"Römhild, Roderich, and Dan I. Andersson. “Mechanisms and Therapeutic Potential of Collateral Sensitivity to Antibiotics.” <i>PLoS Pathogens</i>, vol. 17, no. 1, e1009172, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>.","apa":"Römhild, R., &#38; Andersson, D. I. (2021). Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1009172\">https://doi.org/10.1371/journal.ppat.1009172</a>","ista":"Römhild R, Andersson DI. 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. PLoS Pathogens. 17(1), e1009172.","ama":"Römhild R, Andersson DI. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics. <i>PLoS Pathogens</i>. 2021;17(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1009172\">10.1371/journal.ppat.1009172</a>","ieee":"R. Römhild and D. I. Andersson, “Mechanisms and therapeutic potential of collateral sensitivity to antibiotics,” <i>PLoS Pathogens</i>, vol. 17, no. 1. Public Library of Science, 2021.","short":"R. Römhild, D.I. Andersson, PLoS Pathogens 17 (2021)."},"doi":"10.1371/journal.ppat.1009172","publication_status":"published","date_published":"2021-01-14T00:00:00Z","oa_version":"Published Version","publication_identifier":{"issn":["15537366"],"eissn":["15537374"]},"oa":1,"status":"public","month":"01","year":"2021","issue":"1","date_updated":"2023-08-07T13:36:55Z","_id":"9046","article_number":"e1009172","article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":17,"external_id":{"isi":["000610190400007"],"pmid":["33444399"]},"publication":"PLoS Pathogens","date_created":"2021-01-31T23:01:21Z","has_accepted_license":"1","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"Mechanisms and therapeutic potential of collateral sensitivity to antibiotics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Public Library of Science","day":"14","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"acknowledgement":"Our work was supported by the Swedish Research Council (grant 2017-01527) to DIA","file":[{"date_created":"2021-02-03T12:13:03Z","date_updated":"2021-02-03T12:13:03Z","file_name":"2021_PlosPathogens_Roemhild.pdf","access_level":"open_access","checksum":"d745d7f8fcbb9b95fea16a36f94dee31","file_id":"9070","creator":"dernst","file_size":570066,"success":1,"relation":"main_file","content_type":"application/pdf"}],"isi":1,"author":[{"first_name":"Roderich","orcid":"0000-0001-9480-5261","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","last_name":"Römhild","full_name":"Römhild, Roderich"},{"last_name":"Andersson","first_name":"Dan I.","full_name":"Andersson, Dan I."}]},{"article_type":"original","article_processing_charge":"No","external_id":{"arxiv":["1909.04892"],"isi":["000607808800002"]},"quality_controlled":"1","volume":20,"related_material":{"record":[{"id":"8536","status":"public","relation":"earlier_version"}]},"date_created":"2021-01-31T23:01:21Z","page":"18-27","publication":"IEEE Transactions on Wireless Communications","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"MaMo"}],"publisher":"IEEE","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Sublinear latency for simplified successive cancellation decoding of polar codes","acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162, and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei. The authors would like to thank the anonymous reviewers for their comments that helped improving the quality of the manuscript.","day":"01","author":[{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco"},{"full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali","last_name":"Hashemi"},{"full_name":"Cioffi, John M.","last_name":"Cioffi","first_name":"John M."},{"full_name":"Goldsmith, Andrea","last_name":"Goldsmith","first_name":"Andrea"}],"isi":1,"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1909.04892","open_access":"1"}],"citation":{"apa":"Mondelli, M., Hashemi, S. A., Cioffi, J. M., &#38; Goldsmith, A. (2021). Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>","ista":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. 2021. Sublinear latency for simplified successive cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 20(1), 18–27.","mla":"Mondelli, Marco, et al. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1, IEEE, 2021, pp. 18–27, doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>.","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John M. Cioffi, and Andrea Goldsmith. “Sublinear Latency for Simplified Successive Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/TWC.2020.3022922\">https://doi.org/10.1109/TWC.2020.3022922</a>.","short":"M. Mondelli, S.A. Hashemi, J.M. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 20 (2021) 18–27.","ieee":"M. Mondelli, S. A. Hashemi, J. M. Cioffi, and A. Goldsmith, “Sublinear latency for simplified successive cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 20, no. 1. IEEE, pp. 18–27, 2021.","ama":"Mondelli M, Hashemi SA, Cioffi JM, Goldsmith A. Sublinear latency for simplified successive cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2021;20(1):18-27. doi:<a href=\"https://doi.org/10.1109/TWC.2020.3022922\">10.1109/TWC.2020.3022922</a>"},"intvolume":"        20","publication_status":"published","doi":"10.1109/TWC.2020.3022922","oa_version":"Preprint","date_published":"2021-01-01T00:00:00Z","status":"public","publication_identifier":{"issn":["15361276"],"eissn":["15582248"]},"oa":1,"month":"01","date_updated":"2023-08-07T13:36:25Z","abstract":[{"text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.","lang":"eng"}],"arxiv":1,"issue":"1","year":"2021","_id":"9047"},{"date_created":"2021-02-01T09:20:00Z","publication":"Physical Review Letters","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"type":"journal_article","article_processing_charge":"Yes","article_type":"original","external_id":{"isi":["000613148200001"],"arxiv":["2008.04894"]},"quality_controlled":"1","keyword":["General Physics and Astronomy"],"volume":126,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"29","acknowledgement":"S. D. N. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. M. and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and\r\nInnovation Programme (Grant Agreement No. 850899).","file":[{"relation":"main_file","content_type":"application/pdf","file_size":398075,"success":1,"file_name":"2021_PhysicalRevLett_DeNicola.pdf","date_updated":"2021-02-03T12:47:04Z","date_created":"2021-02-03T12:47:04Z","checksum":"d9acbc502390ed7a97e631d23ae19ecd","file_id":"9074","creator":"dernst","access_level":"open_access"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"author":[{"full_name":"De Nicola, Stefano","orcid":"0000-0002-4842-6671","first_name":"Stefano","last_name":"De Nicola","id":"42832B76-F248-11E8-B48F-1D18A9856A87"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym"}],"isi":1,"title":"Entanglement view of dynamical quantum phase transitions","publisher":"American Physical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","doi":"10.1103/physrevlett.126.040602","date_published":"2021-01-29T00:00:00Z","oa_version":"Published Version","ddc":["530"],"file_date_updated":"2021-02-03T12:47:04Z","intvolume":"       126","citation":{"chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>.","apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2021). Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.126.040602\">https://doi.org/10.1103/physrevlett.126.040602</a>","ista":"De Nicola S, Michailidis A, Serbyn M. 2021. Entanglement view of dynamical quantum phase transitions. Physical Review Letters. 126(4), 040602.","mla":"De Nicola, Stefano, et al. “Entanglement View of Dynamical Quantum Phase Transitions.” <i>Physical Review Letters</i>, vol. 126, no. 4, 040602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>.","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement view of dynamical quantum phase transitions,” <i>Physical Review Letters</i>, vol. 126, no. 4. American Physical Society, 2021.","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement view of dynamical quantum phase transitions. <i>Physical Review Letters</i>. 2021;126(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.126.040602\">10.1103/physrevlett.126.040602</a>","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review Letters 126 (2021)."},"year":"2021","date_updated":"2023-09-05T12:08:58Z","issue":"4","abstract":[{"text":"The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.","lang":"eng"}],"arxiv":1,"_id":"9048","article_number":"040602","oa":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"status":"public","ec_funded":1,"month":"01"},{"oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","month":"02","year":"2021","date_updated":"2023-09-07T13:29:01Z","abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"_id":"9056","place":"Klosterneuburg","ddc":["006","514","516"],"file_date_updated":"2021-02-03T10:37:28Z","citation":{"chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>.","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","mla":"Osang, Georg F. <i>Multi-Cover Persistence and Delaunay Mosaics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>.","apa":"Osang, G. F. (2021). <i>Multi-cover persistence and Delaunay mosaics</i>. Institute of Science and Technology Austria, Klosterneuburg. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021."},"publication_status":"published","doi":"10.15479/AT:ISTA:9056","date_published":"2021-02-01T00:00:00Z","oa_version":"Published Version","title":"Multi-cover persistence and Delaunay mosaics","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","file":[{"access_level":"closed","file_id":"9063","creator":"patrickd","checksum":"bcf27986147cab0533b6abadd74e7629","date_created":"2021-02-02T14:09:25Z","date_updated":"2021-02-03T10:37:28Z","file_name":"thesis_source.zip","file_size":13446994,"relation":"source_file","content_type":"application/zip"},{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":5210329,"file_name":"thesis_pdfA2b.pdf","date_updated":"2021-02-02T14:09:18Z","date_created":"2021-02-02T14:09:18Z","creator":"patrickd","file_id":"9064","checksum":"9cc8af266579a464385bbe2aff6af606","access_level":"open_access"}],"author":[{"orcid":"0000-0002-8882-5116","first_name":"Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F"}],"article_processing_charge":"No","related_material":{"record":[{"id":"187","status":"public","relation":"part_of_dissertation"},{"id":"8703","relation":"part_of_dissertation","status":"public"}]},"page":"134","date_created":"2021-02-02T14:11:06Z","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"},{"_id":"GradSch"}],"type":"dissertation"},{"date_published":"2021-02-03T00:00:00Z","oa_version":"Published Version","doi":"10.1523/jneurosci.1655-20.2020","publication_status":"published","citation":{"short":"I.L. Hanganu-Opatz, S.J.B. Butt, S. Hippenmeyer, N.V. De Marco García, J.A. Cardin, B. Voytek, A.R. Muotri, The Journal of Neuroscience 41 (2021) 813–822.","ieee":"I. L. Hanganu-Opatz <i>et al.</i>, “The logic of developing neocortical circuits in health and disease,” <i>The Journal of Neuroscience</i>, vol. 41, no. 5. Society for Neuroscience, pp. 813–822, 2021.","ama":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, et al. The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. 2021;41(5):813-822. doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>","ista":"Hanganu-Opatz IL, Butt SJB, Hippenmeyer S, De Marco García NV, Cardin JA, Voytek B, Muotri AR. 2021. The logic of developing neocortical circuits in health and disease. The Journal of Neuroscience. 41(5), 813–822.","mla":"Hanganu-Opatz, Ileana L., et al. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>, vol. 41, no. 5, Society for Neuroscience, 2021, pp. 813–22, doi:<a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">10.1523/jneurosci.1655-20.2020</a>.","apa":"Hanganu-Opatz, I. L., Butt, S. J. B., Hippenmeyer, S., De Marco García, N. V., Cardin, J. A., Voytek, B., &#38; Muotri, A. R. (2021). The logic of developing neocortical circuits in health and disease. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>","chicago":"Hanganu-Opatz, Ileana L., Simon J. B. Butt, Simon Hippenmeyer, Natalia V. De Marco García, Jessica A. Cardin, Bradley Voytek, and Alysson R. Muotri. “The Logic of Developing Neocortical Circuits in Health and Disease.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2021. <a href=\"https://doi.org/10.1523/jneurosci.1655-20.2020\">https://doi.org/10.1523/jneurosci.1655-20.2020</a>."},"intvolume":"        41","ddc":["570"],"scopus_import":"1","file_date_updated":"2022-05-27T06:59:55Z","_id":"9073","year":"2021","abstract":[{"text":"The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention.","lang":"eng"}],"issue":"5","date_updated":"2023-09-05T14:03:17Z","ec_funded":1,"month":"02","oa":1,"publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"status":"public","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"The Journal of Neuroscience","page":"813-822","date_created":"2021-02-03T12:23:51Z","has_accepted_license":"1","volume":41,"keyword":["General Neuroscience"],"quality_controlled":"1","external_id":{"pmid":["33431633"],"isi":["000616763400002"]},"article_type":"original","article_processing_charge":"No","file":[{"content_type":"application/pdf","relation":"main_file","file_size":1031150,"success":1,"date_updated":"2022-05-27T06:59:55Z","file_name":"2021_JourNeuroscience_Hanganu.pdf","date_created":"2022-05-27T06:59:55Z","checksum":"578fd7ed1a0aef74bce61bea2d987b33","file_id":"11414","creator":"dernst","access_level":"open_access"}],"isi":1,"author":[{"last_name":"Hanganu-Opatz","first_name":"Ileana L.","full_name":"Hanganu-Opatz, Ileana L."},{"first_name":"Simon J. B.","last_name":"Butt","full_name":"Butt, Simon J. B."},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"full_name":"De Marco García, Natalia V.","first_name":"Natalia V.","last_name":"De Marco García"},{"first_name":"Jessica A.","last_name":"Cardin","full_name":"Cardin, Jessica A."},{"last_name":"Voytek","first_name":"Bradley","full_name":"Voytek, Bradley"},{"full_name":"Muotri, Alysson R.","last_name":"Muotri","first_name":"Alysson R."}],"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"day":"03","pmid":1,"acknowledgement":"Work in the I.L.H.-O. laboratory was supported by European Research Council Grant ERC-2015-CoG 681577 and German Research Foundation Ha 4466/10-1, Ha4466/11-1, Ha4466/12-1, SPP 1665, and SFB 936B5. Work in the S.J.B.B. laboratory was supported by Biotechnology and Biological Sciences Research Council BB/P003796/1, Medical Research Council MR/K004387/1 and MR/T033320/1, Wellcome Trust 215199/Z/19/Z and 102386/Z/13/Z, and John Fell Fund. Work in the S.H. laboratory was supported by European Research Council Grants ERC-2016-CoG 725780 LinPro and FWF SFB F78. This work was supported by National Institutes of Health Grant NIMH 1R01MH110553 to N.V.D.M.G. Work in the J.A.C. laboratory was supported by the Ludwig Family Foundation, Simons Foundation SFARI Research Award, and National Institutes of Health/National Institute of Mental Health R01 MH102365 and R01MH113852. The B.V. laboratory was supported by Whitehall Foundation 2017-12-73, National Science Foundation 1736028, National Institutes of Health, National Institute of General Medical Sciences R01GM134363-01, and Halıcıoğlu Data Science Institute Fellowship. This work was supported by the University of California San Diego School of Medicine.","title":"The logic of developing neocortical circuits in health and disease","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Society for Neuroscience"},{"doi":"10.1101/2020.12.31.425016","publication_status":"submitted","publication":"bioRxiv","date_created":"2021-02-04T07:23:23Z","oa_version":"Preprint","type":"preprint","department":[{"_id":"SiHi"}],"date_published":"2021-01-01T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2020.12.31.425016","open_access":"1"}],"citation":{"short":"D.J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, BioRxiv (n.d.).","ama":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>","ieee":"D. J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous identification of brain cell type and lineage via single cell RNA sequencing,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. bioRxiv, <a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","apa":"Anderson, D. J., Pauler, F., McKenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (n.d.). Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>","mla":"Anderson, Donovan J., et al. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","chicago":"Anderson, Donovan J., Florian Pauler, Aaron McKenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>."},"acknowledgement":"We thank Bill Bolosky, Microsoft Research, for earlier work showing proof of concept in TCGA\r\nbulk RNA-seq data. Supported by the Paul G. Allen Frontiers Group (University of Washington);\r\nNIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant\r\n(C13-002) to SH, and the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation program 725780 LinPro to SH.","abstract":[{"lang":"eng","text":"Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans."}],"date_updated":"2021-02-04T07:29:53Z","year":"2021","day":"01","author":[{"full_name":"Anderson, Donovan J.","last_name":"Anderson","first_name":"Donovan J."},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian"},{"first_name":"Aaron","last_name":"McKenna","full_name":"McKenna, Aaron"},{"full_name":"Shendure, Jay","first_name":"Jay","last_name":"Shendure"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Horwitz, Marshall S.","last_name":"Horwitz","first_name":"Marshall S."}],"project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"_id":"9082","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Cold Spring Harbor Laboratory","oa":1,"title":"Simultaneous identification of brain cell type and lineage via single cell RNA sequencing","month":"01","ec_funded":1}]