[{"date_published":"2018-04-15T00:00:00Z","citation":{"mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","apa":"Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press."},"publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","page":"464-472","article_processing_charge":"No","day":"15","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14201","intvolume":" 84","title":"Boosting variational inference: An optimization perspective","status":"public","abstract":[{"text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties.","lang":"eng"}],"type":"conference","alternative_title":["PMLR"],"conference":{"end_date":"2018-04-11","start_date":"2018-04-09","location":"Playa Blanca, Lanzarote","name":"AISTATS: Conference on Artificial Intelligence and Statistics"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1708.01733","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1708.01733"]},"quality_controlled":"1","month":"04","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"last_name":"Khanna","first_name":"Rajiv","full_name":"Khanna, Rajiv"},{"first_name":"Joydeep","last_name":"Ghosh","full_name":"Ghosh, Joydeep"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"volume":84,"date_created":"2023-08-22T14:15:20Z","date_updated":"2023-09-13T07:52:40Z","year":"2018","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"publication_status":"published","extern":"1"},{"type":"conference","extern":"1","abstract":[{"text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data.","lang":"eng"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","publication_status":"published","status":"public","department":[{"_id":"FrLo"}],"_id":"14198","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T06:35:12Z","date_created":"2023-08-22T14:12:48Z","oa_version":"Preprint","author":[{"first_name":"Vincent","last_name":"Fortuin","full_name":"Fortuin, Vincent"},{"full_name":"Hüser, Matthias","last_name":"Hüser","first_name":"Matthias"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"first_name":"Heiko","last_name":"Strathmann","full_name":"Strathmann, Heiko"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"}],"day":"06","month":"06","article_processing_charge":"No","quality_controlled":"1","publication":"International Conference on Learning Representations","main_file_link":[{"url":"https://arxiv.org/abs/1806.02199","open_access":"1"}],"oa":1,"citation":{"ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018."},"external_id":{"arxiv":["1806.02199"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-05-09","start_date":"2019-05-06","location":"New Orleans, LA, United States","name":"ICLR: International Conference on Learning Representations"},"date_published":"2018-06-06T00:00:00Z"},{"month":"07","language":[{"iso":"eng"}],"conference":{"start_date":"2018-07-10","location":"Stockholm, Sweden","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08544"}],"external_id":{"arxiv":["1804.08544"]},"oa":1,"extern":"1","volume":80,"date_updated":"2023-09-13T08:13:39Z","date_created":"2023-08-22T14:16:01Z","author":[{"last_name":"Yurtsever","first_name":"Alp","full_name":"Yurtsever, Alp"},{"first_name":"Olivier","last_name":"Fercoq","full_name":"Fercoq, Olivier"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"},{"full_name":"Cevher, Volkan","last_name":"Cevher","first_name":"Volkan"}],"department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published","year":"2018","article_processing_charge":"No","day":"15","date_published":"2018-07-15T00:00:00Z","page":"5727-5736","citation":{"ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736.","ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736.","chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018."},"publication":"Proceedings of the 35th International Conference on Machine Learning","abstract":[{"lang":"eng","text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework."}],"alternative_title":["PMLR"],"type":"conference","oa_version":"Preprint","intvolume":" 80","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","status":"public","_id":"14203","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"08","external_id":{"isi":["000440014100020"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"isi":1,"quality_controlled":"1","doi":"10.1534/genetics.118.301018","language":[{"iso":"eng"}],"publist_id":"7617","year":"2018","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"volume":209,"date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:22:32Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018."},"publication":"Genetics","page":"1279 - 1303","date_published":"2018-08-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"_id":"282","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 209","status":"public","title":"Introgression of a block of genome under infinitesimal selection","oa_version":"Submitted Version"},{"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2017/507","open_access":"1"}],"oa":1,"external_id":{"isi":["000448139300368"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2018-06-22","location":"Vail, CO, USA","start_date":"2018-06-17 ","name":"ISIT: International Symposium on Information Theory"},"doi":"10.1109/ISIT.2018.8437654","month":"08","publication_status":"published","publisher":"IEEE","department":[{"_id":"KrPi"}],"year":"2018","date_updated":"2023-09-13T08:23:18Z","date_created":"2018-12-11T11:44:40Z","volume":2018,"author":[{"last_name":"Obremski","first_name":"Marciej","full_name":"Obremski, Marciej"},{"first_name":"Maciej","last_name":"Skorski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skorski, Maciej"}],"publist_id":"7946","citation":{"chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654"},"date_published":"2018-08-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","title":"Inverted leftover hash lemma","status":"public","intvolume":" 2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"108","oa_version":"Submitted Version","alternative_title":["ISIT Proceedings"],"type":"conference","abstract":[{"text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes.","lang":"eng"}]},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-01T00:00:00Z","page":"3198-3207","publication":"Proceedings of the 35th International Conference on Machine Learning","citation":{"ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press.","ieee":"F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207.","short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207."},"abstract":[{"lang":"eng","text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives."}],"alternative_title":["PMLR"],"type":"conference","oa_version":"Preprint","title":"On matching pursuit and coordinate descent","status":"public","intvolume":" 80","_id":"14204","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.09539"}],"external_id":{"arxiv":["1803.09539"]},"oa":1,"extern":"1","date_updated":"2023-09-13T08:19:05Z","date_created":"2023-08-22T14:16:25Z","volume":80,"author":[{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Raj, Anant","last_name":"Raj","first_name":"Anant"},{"last_name":"Karimireddy","first_name":"Sai Praneeth","full_name":"Karimireddy, Sai Praneeth"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Stich, Sebastian U.","first_name":"Sebastian U.","last_name":"Stich"},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"year":"2018"},{"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:45:04Z","publist_id":"7761","date_updated":"2023-09-13T08:45:09Z","date_created":"2018-12-11T11:44:57Z","volume":10981,"author":[{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","first_name":"Bernhard"},{"full_name":"Qadeer, Shaz","first_name":"Shaz","last_name":"Qadeer"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","year":"2018","month":"07","language":[{"iso":"eng"}],"conference":{"start_date":"2018-07-14","location":"Oxford, UK","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-319-96145-3_5","isi":1,"quality_controlled":"1","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491481600005"]},"abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","file":[{"checksum":"c64fff560fe5a7532ec10626ad1c215e","date_created":"2018-12-17T12:52:12Z","date_updated":"2020-07-14T12:45:04Z","relation":"main_file","file_id":"5705","content_type":"application/pdf","file_size":1603844,"creator":"dernst","access_level":"open_access","file_name":"2018_LNCS_Kragl.pdf"}],"oa_version":"Published Version","title":"Layered Concurrent Programs","ddc":["000"],"status":"public","intvolume":" 10981","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"160","day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-18T00:00:00Z","page":"79 - 102","citation":{"chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5"}},{"month":"08","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000443383300024"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pbio.2005971","language":[{"iso":"eng"}],"article_number":"2005971","file_date_updated":"2020-07-14T12:48:10Z","publist_id":"7972","year":"2018","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"author":[{"full_name":"Chaudhry, Waqas","first_name":"Waqas","last_name":"Chaudhry"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros"},{"full_name":"Shah, Nilang","last_name":"Shah","first_name":"Nilang"},{"last_name":"Weiss","first_name":"Howard","full_name":"Weiss, Howard"},{"last_name":"Mccall","first_name":"Ingrid","full_name":"Mccall, Ingrid"},{"full_name":"Meyer, Justin","first_name":"Justin","last_name":"Meyer"},{"last_name":"Gupta","first_name":"Animesh","full_name":"Gupta, Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"},{"last_name":"Levin","first_name":"Bruce","full_name":"Levin, Bruce"}],"related_material":{"record":[{"id":"9810","status":"public","relation":"research_data"}]},"date_created":"2018-12-11T11:44:32Z","date_updated":"2023-09-13T08:45:41Z","volume":16,"scopus_import":"1","day":"16","has_accepted_license":"1","article_processing_charge":"Yes","publication":"PLoS Biology","citation":{"short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971."},"date_published":"2018-08-16T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”."}],"issue":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"82","status":"public","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","ddc":["570"],"intvolume":" 16","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5706","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-17T12:55:31Z","checksum":"527076f78265cd4ea192cd1569851587","file_name":"2018_Plos_Chaudhry.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4007095,"creator":"dernst"}]},{"month":"08","oa":1,"external_id":{"isi":["000448185000050"]},"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"isi":1,"quality_controlled":"1","doi":"10.1145/3197517.3201325","language":[{"iso":"eng"}],"article_number":"89","ec_funded":1,"publist_id":"8053","file_date_updated":"2020-07-14T12:46:22Z","year":"2018","department":[{"_id":"BeBi"}],"publisher":"ACM","publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/"}]},"author":[{"last_name":"Umetani","first_name":"Nobuyuki","full_name":"Umetani, Nobuyuki"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"volume":37,"date_updated":"2023-09-13T08:46:15Z","date_created":"2018-12-11T11:44:06Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"04","citation":{"ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018)."},"publication":"ACM Trans. Graph.","date_published":"2018-08-04T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"4","intvolume":" 37","status":"public","ddc":["003","004"],"title":"Learning three-dimensional flow for interactive aerodynamic design","pubrep_id":"1049","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5216","date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:16:28Z","checksum":"7a2243668f215821bc6aecad0320079a","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","access_level":"open_access","content_type":"application/pdf","file_size":22803163,"creator":"system"}]},{"date_published":"2018-03-03T00:00:00Z","article_type":"original","page":"148-203","publication":"Annals Applied Probability ","citation":{"chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/17-AAP1302.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.","mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:10.1214/17-AAP1302.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular law. Annals Applied Probability . Institute of Mathematical Statistics. https://doi.org/10.1214/17-AAP1302","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203.","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302"},"day":"03","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Local inhomogeneous circular law","status":"public","intvolume":" 28","_id":"566","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n"}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1214/17-AAP1302","quality_controlled":"1","isi":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"oa":1,"external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.07776 "}],"month":"03","date_created":"2018-12-11T11:47:13Z","date_updated":"2023-09-13T08:47:52Z","volume":28,"author":[{"first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","year":"2018","ec_funded":1},{"publist_id":"7948","year":"2018","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"first_name":"Anton","last_name":"Petrunin","full_name":"Petrunin, Anton"}],"volume":40,"date_created":"2018-12-11T11:44:40Z","date_updated":"2023-09-13T08:49:16Z","month":"09","oa":1,"external_id":{"isi":["000444141200005"],"arxiv":["1702.05172"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00283-018-9795-5","language":[{"iso":"eng"}],"type":"journal_article","issue":"3","abstract":[{"text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"106","intvolume":" 40","status":"public","title":"Long geodesics on convex surfaces","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","apa":"Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.","mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5."},"publication":"Mathematical Intelligencer","page":"26 - 31","date_published":"2018-09-01T00:00:00Z"},{"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-17T12:50:07Z","checksum":"9c7eba51a35c62da8c13f98120b64df4","relation":"main_file","file_id":"5704","file_size":2252043,"content_type":"application/pdf","creator":"dernst","file_name":"2018_JournalCellBiology_Brown.pdf","access_level":"open_access"}],"intvolume":" 217","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","status":"public","ddc":["570"],"_id":"275","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"6","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"type":"journal_article","date_published":"2018-04-12T00:00:00Z","page":"2205 - 2221","citation":{"apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051","ieee":"M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051."},"publication":"Journal of Cell Biology","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1","volume":217,"date_created":"2018-12-11T11:45:33Z","date_updated":"2023-09-13T08:51:29Z","author":[{"full_name":"Brown, Markus","last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Louise","first_name":"Louise","last_name":"Johnson"},{"full_name":"Leone, Dario","first_name":"Dario","last_name":"Leone"},{"last_name":"Májek","first_name":"Peter","full_name":"Májek, Peter"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","first_name":"Kari","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari"},{"full_name":"Senfter, Daniel","last_name":"Senfter","first_name":"Daniel"},{"full_name":"Bukosza, Nora","last_name":"Bukosza","first_name":"Nora"},{"full_name":"Schachner, Helga","last_name":"Schachner","first_name":"Helga"},{"first_name":"Gabriele","last_name":"Asfour","full_name":"Asfour, Gabriele"},{"first_name":"Brigitte","last_name":"Langer","full_name":"Langer, Brigitte"},{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"full_name":"Parapatics, Katja","last_name":"Parapatics","first_name":"Katja"},{"full_name":"Hong, Young","first_name":"Young","last_name":"Hong"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"last_name":"Kain","first_name":"Renate","full_name":"Kain, Renate"},{"first_name":"Michael","last_name":"Detmar","full_name":"Detmar, Michael"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"David","last_name":"Jackson","full_name":"Jackson, David"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"}],"publisher":"Rockefeller University Press","department":[{"_id":"MiSi"},{"_id":"Bio"}],"publication_status":"published","pmid":1,"acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","year":"2018","publist_id":"7627","ec_funded":1,"file_date_updated":"2020-07-14T12:45:45Z","language":[{"iso":"eng"}],"doi":"10.1083/jcb.201612051","project":[{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"oa":1,"month":"04"},{"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","status":"public","intvolume":" 4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"158","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development.","lang":"eng"}],"issue":"8","page":"548 - 553","publication":"Nature Plants","citation":{"short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z","ieee":"H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553."},"date_published":"2018-07-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","year":"2018","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","pmid":1,"date_created":"2018-12-11T11:44:56Z","date_updated":"2023-09-13T08:53:28Z","volume":4,"author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"first_name":"Chulmin","last_name":"Park","full_name":"Park, Chulmin"},{"full_name":"Gutièrrez, Carla","last_name":"Gutièrrez","first_name":"Carla"},{"full_name":"Wójcikowska, Barbara","first_name":"Barbara","last_name":"Wójcikowska"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Chen, Junyi","first_name":"Junyi","last_name":"Chen"},{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"first_name":"Thomas","last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Laux, Thomas","first_name":"Thomas","last_name":"Laux"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/"}]},"ec_funded":1,"publist_id":"7763","quality_controlled":"1","isi":1,"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211"}],"oa":1,"external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0204-z","month":"07"},{"quality_controlled":"1","isi":1,"external_id":{"isi":["000445118200007"]},"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"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tcb.2018.06.006","month":"07","department":[{"_id":"LeSa"}],"publisher":"Elsevier","publication_status":"published","year":"2018","volume":28,"date_created":"2018-12-11T11:44:54Z","date_updated":"2023-09-13T08:51:56Z","author":[{"full_name":"Fiedorczuk, Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol","last_name":"Fiedorczuk"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publist_id":"7769","file_date_updated":"2020-07-14T12:45:00Z","page":"835 - 867","article_type":"original","citation":{"apa":"Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006."},"publication":"Trends in Cell Biology","date_published":"2018-07-26T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","intvolume":" 28","title":"Mammalian mitochondrial complex I structure and disease causing mutations","ddc":["572"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"152","file":[{"date_created":"2019-11-07T12:55:20Z","date_updated":"2020-07-14T12:45:00Z","checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","file_id":"6994","file_size":2185385,"content_type":"application/pdf","creator":"lsazanov","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context."}]},{"month":"01","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1711.09148","open_access":"1"}],"external_id":{"arxiv":["1711.09148"],"isi":["000483921200152"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"New Orleans, Louisiana, United States","start_date":"2018-01-07","end_date":"2018-01-10"},"doi":"10.1137/1.9781611975031.151","publist_id":"7555","ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"ACM","year":"2018","date_created":"2018-12-11T11:45:45Z","date_updated":"2023-09-13T08:50:16Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvorák, Wolfgang","first_name":"Wolfgang","last_name":"Dvorák"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"scopus_import":"1","day":"01","article_processing_charge":"No","page":"2341 - 2356","citation":{"short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356.","mla":"Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356."},"date_published":"2018-01-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components."}],"title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","status":"public","_id":"310","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint"},{"article_processing_charge":"No","day":"07","scopus_import":"1","date_published":"2018-02-07T00:00:00Z","citation":{"ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018.","apa":"Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601","chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601.","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018)."},"publication":"Physical Review Letters","issue":"6","abstract":[{"lang":"eng","text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits."}],"type":"journal_article","oa_version":"Preprint","_id":"436","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 120","status":"public","title":"Manipulating the flow of thermal noise in quantum devices","month":"02","doi":"10.1103/PhysRevLett.120.060601","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09051"}],"external_id":{"isi":["000424382100004"],"arxiv":["1706.09051"]},"oa":1,"project":[{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies"},{"call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438"}],"isi":1,"quality_controlled":"1","publist_id":"7387","ec_funded":1,"article_number":"060601 ","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/"}]},"author":[{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"full_name":"Xuereb, André","last_name":"Xuereb","first_name":"André"}],"volume":120,"date_updated":"2023-09-13T08:52:27Z","date_created":"2018-12-11T11:46:28Z","year":"2018","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","publication_status":"published"},{"file":[{"file_name":"2018_Interface_Hross.pdf","access_level":"open_access","creator":"dernst","file_size":1464288,"content_type":"application/pdf","file_id":"5925","relation":"main_file","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T14:46:44Z","checksum":"56eb4308a15b7190bff938fab1f780e8"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5858","intvolume":" 15","status":"public","title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","ddc":["570"],"issue":"149","abstract":[{"lang":"eng","text":"Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights."}],"type":"journal_article","date_published":"2018-12-05T00:00:00Z","citation":{"mla":"Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600.","short":"S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018).","chicago":"Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600.","ama":"Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600","ista":"Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600.","ieee":"S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","apa":"Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600"},"publication":"Journal of the Royal Society Interface","has_accepted_license":"1","article_processing_charge":"No","day":"05","scopus_import":"1","author":[{"full_name":"Hross, Sabrina","first_name":"Sabrina","last_name":"Hross"},{"last_name":"Theis","first_name":"Fabian J.","full_name":"Theis, Fabian J."},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"Jan","last_name":"Hasenauer","full_name":"Hasenauer, Jan"}],"volume":15,"date_created":"2019-01-20T22:59:18Z","date_updated":"2023-09-13T08:55:05Z","year":"2018","department":[{"_id":"MiSi"}],"publisher":"Royal Society Publishing","publication_status":"published","file_date_updated":"2020-07-14T12:47:13Z","article_number":"20180600","doi":"10.1098/rsif.2018.0600","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000456783800011"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["17425689"]},"month":"12"},{"month":"10","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000447469200001"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.3.103303","article_number":"103303","publist_id":"8039","ec_funded":1,"file_date_updated":"2020-07-14T12:45:04Z","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2018","acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","volume":3,"date_created":"2018-12-11T11:44:10Z","date_updated":"2023-09-13T08:57:05Z","author":[{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999"},{"last_name":"Steinberg","first_name":"Victor","full_name":"Steinberg, Victor"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"16","article_type":"original","citation":{"short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","apa":"Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303."},"publication":"Physical Review Fluids","date_published":"2018-10-16T00:00:00Z","type":"journal_article","issue":"10","abstract":[{"text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives.","lang":"eng"}],"intvolume":" 3","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","ddc":["532"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"16","file":[{"access_level":"open_access","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","creator":"system","file_size":1838431,"content_type":"application/pdf","file_id":"5043","relation":"main_file","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","date_created":"2018-12-12T10:13:56Z","date_updated":"2020-07-14T12:45:04Z"}],"oa_version":"Submitted Version","pubrep_id":"1062"},{"date_published":"2018-10-02T00:00:00Z","page":"10690 - 10695","citation":{"chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115.","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115.","apa":"Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115","ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695.","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115"},"publication":"PNAS","has_accepted_license":"1","article_processing_charge":"No","day":"02","scopus_import":"1","file":[{"file_size":4070777,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_PNAS_Rybicki.pdf","checksum":"df7ac544a587c06b75692653b9fabd18","date_created":"2019-04-09T08:02:50Z","date_updated":"2020-07-14T12:46:26Z","relation":"main_file","file_id":"6258"}],"oa_version":"Submitted Version","pubrep_id":"1063","intvolume":" 115","ddc":["570","577"],"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","status":"public","_id":"43","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"42","abstract":[{"text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1721061115","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000447491300057"]},"month":"10","volume":115,"date_created":"2018-12-11T11:44:19Z","date_updated":"2023-09-13T08:57:38Z","author":[{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki"},{"first_name":"Eva","last_name":"Kisdi","full_name":"Kisdi, Eva"},{"first_name":"Jani","last_name":"Anttila","full_name":"Anttila, Jani"}],"publisher":"National Academy of Sciences","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2018","acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","publist_id":"8011","ec_funded":1,"file_date_updated":"2020-07-14T12:46:26Z"},{"file_date_updated":"2020-07-14T12:44:43Z","ec_funded":1,"publist_id":"8043","article_number":"136","date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-13T08:56:07Z","volume":37,"author":[{"last_name":"Alderighi","first_name":"Thomas","full_name":"Alderighi, Thomas"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"first_name":"Daniela","last_name":"Giorgi","full_name":"Giorgi, Daniela"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"ACM","year":"2018","month":"08","language":[{"iso":"eng"}],"doi":"10.1145/3197517.3201381","quality_controlled":"1","isi":1,"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"external_id":{"isi":["000448185000097"]},"oa":1,"abstract":[{"lang":"eng","text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery."}],"issue":"4","type":"journal_article","file":[{"access_level":"open_access","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","file_size":91939066,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5374","checksum":"61d46273dca4de626accef1d17a0aaad","date_created":"2018-12-12T10:18:52Z","date_updated":"2020-07-14T12:44:43Z"}],"oa_version":"Submitted Version","pubrep_id":"1038","ddc":["004"],"status":"public","title":"Metamolds: Computational design of silicone molds","intvolume":" 37","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"13","day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-08-04T00:00:00Z","publication":"ACM Trans. Graph.","citation":{"short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018).","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136."}}]