[{"volume":15,"date_created":"2019-11-04T15:45:17Z","month":"10","type":"journal_article","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.\r\n"}],"date_updated":"2023-09-15T12:19:31Z","_id":"6982","year":"2019","date_published":"2019-10-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"oa":1,"publication_status":"published","intvolume":"        15","related_material":{"record":[{"id":"309","status":"public","relation":"earlier_version"}]},"citation":{"ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. <i>ACM Transactions on Algorithms</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1145/3344549\">10.1145/3344549</a>","apa":"Akitaya, H., Fulek, R., &#38; Tóth, C. (2019). Recognizing weak embeddings of graphs. <i>ACM Transactions on Algorithms</i>. ACM. <a href=\"https://doi.org/10.1145/3344549\">https://doi.org/10.1145/3344549</a>","ista":"Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 15(4), 50.","mla":"Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” <i>ACM Transactions on Algorithms</i>, vol. 15, no. 4, 50, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3344549\">10.1145/3344549</a>.","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” <i>ACM Transactions on Algorithms</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3344549\">https://doi.org/10.1145/3344549</a>.","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” <i>ACM Transactions on Algorithms</i>, vol. 15, no. 4. ACM, 2019.","short":"H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019)."},"status":"public","external_id":{"arxiv":["1709.09209"]},"article_number":"50","title":"Recognizing weak embeddings of graphs","arxiv":1,"author":[{"last_name":"Akitaya","first_name":"Hugo","full_name":"Akitaya, Hugo"},{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav"},{"last_name":"Tóth","first_name":"Csaba","full_name":"Tóth, Csaba"}],"day":"01","publication":"ACM Transactions on Algorithms","article_type":"original","scopus_import":1,"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"doi":"10.1145/3344549","quality_controlled":"1","issue":"4","language":[{"iso":"eng"}],"project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}]},{"citation":{"ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153.","mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>, vol. 10, 2153, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>.","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., &#38; Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>","ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. 2019;10. doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>","short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019).","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” <i>Frontiers in Immunology</i>, vol. 10. Frontiers, 2019.","chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>."},"intvolume":"        10","external_id":{"pmid":["31616407"],"isi":["000487187000001"]},"status":"public","date_published":"2019-09-20T00:00:00Z","ddc":["570"],"has_accepted_license":"1","publication_status":"published","oa":1,"_id":"6983","year":"2019","date_created":"2019-11-04T15:50:06Z","file_date_updated":"2020-07-14T12:47:46Z","volume":10,"date_updated":"2023-08-30T07:18:23Z","abstract":[{"text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.","lang":"eng"}],"month":"09","oa_version":"Published Version","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","doi":"10.3389/fimmu.2019.02153","publication_identifier":{"issn":["1664-3224"]},"scopus_import":"1","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publication":"Frontiers in Immunology","pmid":1,"department":[{"_id":"BeVi"}],"publisher":"Frontiers","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","article_number":"2153","file":[{"date_created":"2019-11-04T15:54:00Z","access_level":"open_access","date_updated":"2020-07-14T12:47:46Z","file_id":"6984","checksum":"68d1708f7aa412544159b498ef17a6b9","content_type":"application/pdf","relation":"main_file","file_size":2083061,"creator":"dernst","file_name":"2019_FrontiersImmonology_Kelemen.pdf"}],"day":"20","author":[{"last_name":"Kelemen","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K"},{"full_name":"Rajakaruna, H","first_name":"H","last_name":"Rajakaruna"},{"last_name":"Cockburn","first_name":"IA","full_name":"Cockburn, IA"},{"first_name":"VV","last_name":"Ganusov","full_name":"Ganusov, VV"}]},{"external_id":{"arxiv":["1809.03864"]},"status":"public","conference":{"start_date":"2019-07-14","location":"Budapest, Hungary","name":"IJCNN: International Joint Conference on Neural Networks","end_date":"2019-07-19"},"language":[{"iso":"eng"}],"citation":{"ieee":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response characterization for auditing cell dynamics in long short-term memory networks,” in <i>Proceedings of the International Joint Conference on Neural Networks</i>, Budapest, Hungary, 2019.","chicago":"Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu, and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” In <i>Proceedings of the International Joint Conference on Neural Networks</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">https://doi.org/10.1109/ijcnn.2019.8851954</a>.","short":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings of the International Joint Conference on Neural Networks, IEEE, 2019.","ama":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization for auditing cell dynamics in long short-term memory networks. In: <i>Proceedings of the International Joint Conference on Neural Networks</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">10.1109/ijcnn.2019.8851954</a>","mla":"Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” <i>Proceedings of the International Joint Conference on Neural Networks</i>, 8851954, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">10.1109/ijcnn.2019.8851954</a>.","ista":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization for auditing cell dynamics in long short-term memory networks. Proceedings of the International Joint Conference on Neural Networks. IJCNN: International Joint Conference on Neural Networks, 8851954.","apa":"Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., &#38; Rus, D. (2019). Response characterization for auditing cell dynamics in long short-term memory networks. In <i>Proceedings of the International Joint Conference on Neural Networks</i>. Budapest, Hungary: IEEE. <a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">https://doi.org/10.1109/ijcnn.2019.8851954</a>"},"publication_identifier":{"isbn":["9781728119854"]},"publication_status":"published","oa":1,"date_published":"2019-09-30T00:00:00Z","doi":"10.1109/ijcnn.2019.8851954","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.03864","open_access":"1"}],"publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"year":"2019","_id":"6985","publication":"Proceedings of the International Joint Conference on Neural Networks","scopus_import":1,"author":[{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"full_name":"Amini, Alexander","last_name":"Amini","first_name":"Alexander"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"first_name":"Felix","last_name":"Naser","full_name":"Naser, Felix"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"}],"month":"09","oa_version":"Preprint","type":"conference","day":"30","abstract":[{"text":"In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets.","lang":"eng"}],"date_updated":"2021-01-12T08:11:19Z","article_number":"8851954","title":"Response characterization for auditing cell dynamics in long short-term memory networks","arxiv":1,"date_created":"2019-11-04T15:59:58Z"},{"title":"A colimit of traces of reflection groups","arxiv":1,"author":[{"last_name":"Li","first_name":"Penghui","full_name":"Li, Penghui","id":"42A24CCC-F248-11E8-B48F-1D18A9856A87"}],"day":"01","publication":"Proceedings of the American Mathematical Society","article_type":"original","scopus_import":"1","ec_funded":1,"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"AMS","department":[{"_id":"TaHa"}],"doi":"10.1090/proc/14586","quality_controlled":"1","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"isi":1,"issue":"11","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593"}],"volume":147,"date_created":"2019-11-04T16:10:50Z","page":"4597-4604","type":"journal_article","oa_version":"Preprint","month":"11","abstract":[{"lang":"eng","text":"Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. "}],"date_updated":"2023-09-05T12:22:21Z","_id":"6986","year":"2019","date_published":"2019-11-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.07039"}],"publication_status":"published","oa":1,"intvolume":"       147","citation":{"short":"P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604.","ieee":"P. Li, “A colimit of traces of reflection groups,” <i>Proceedings of the American Mathematical Society</i>, vol. 147, no. 11. AMS, pp. 4597–4604, 2019.","chicago":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” <i>Proceedings of the American Mathematical Society</i>. AMS, 2019. <a href=\"https://doi.org/10.1090/proc/14586\">https://doi.org/10.1090/proc/14586</a>.","mla":"Li, Penghui. “A Colimit of Traces of Reflection Groups.” <i>Proceedings of the American Mathematical Society</i>, vol. 147, no. 11, AMS, 2019, pp. 4597–604, doi:<a href=\"https://doi.org/10.1090/proc/14586\">10.1090/proc/14586</a>.","ista":"Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604.","apa":"Li, P. (2019). A colimit of traces of reflection groups. <i>Proceedings of the American Mathematical Society</i>. AMS. <a href=\"https://doi.org/10.1090/proc/14586\">https://doi.org/10.1090/proc/14586</a>","ama":"Li P. A colimit of traces of reflection groups. <i>Proceedings of the American Mathematical Society</i>. 2019;147(11):4597-4604. doi:<a href=\"https://doi.org/10.1090/proc/14586\">10.1090/proc/14586</a>"},"external_id":{"isi":["000488621700004"],"arxiv":["1810.07039"]},"status":"public"},{"publication_identifier":{"issn":["0080-1844"],"eissn":["1861-0412"],"isbn":["9783030234584","9783030234591"]},"doi":"10.1007/978-3-030-23459-1_6","quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"first_name":"Alex","last_name":"McDougall","full_name":"McDougall, Alex"},{"full_name":"Chenevert, Janet","last_name":"Chenevert","first_name":"Janet"},{"last_name":"Godard","first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G"},{"full_name":"Dumollard, Remi","last_name":"Dumollard","first_name":"Remi"}],"file":[{"checksum":"7f43e1e3706d15061475c5c57efc2786","date_updated":"2020-07-14T12:47:46Z","file_id":"7829","access_level":"open_access","date_created":"2020-05-14T10:09:30Z","file_name":"2019_RESULTS_McDougall.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":19317348}],"day":"10","title":"Emergence of embryo shape during cleavage divisions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","pmid":1,"department":[{"_id":"CaHe"}],"publication":"Evo-Devo: Non-model species in cell and developmental biology","article_processing_charge":"No","scopus_import":"1","publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["570"],"date_published":"2019-10-10T00:00:00Z","alternative_title":["RESULTS"],"editor":[{"last_name":"Tworzydlo","first_name":"Waclaw","full_name":"Tworzydlo, Waclaw"},{"last_name":"Bilinski","first_name":"Szczepan M.","full_name":"Bilinski, Szczepan M."}],"status":"public","external_id":{"pmid":["31598855"]},"intvolume":"        68","citation":{"apa":"McDougall, A., Chenevert, J., Godard, B. G., &#38; Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo &#38; S. M. Bilinski (Eds.), <i>Evo-Devo: Non-model species in cell and developmental biology</i> (Vol. 68, pp. 127–154). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">https://doi.org/10.1007/978-3-030-23459-1_6</a>","mla":"McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:<a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">10.1007/978-3-030-23459-1_6</a>.","ista":"McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154.","ama":"McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>. Vol 68. Springer Nature; 2019:127-154. doi:<a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">10.1007/978-3-030-23459-1_6</a>","short":"A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.","chicago":"McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">https://doi.org/10.1007/978-3-030-23459-1_6</a>.","ieee":"A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in <i>Evo-Devo: Non-model species in cell and developmental biology</i>, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154."},"page":"127-154","date_updated":"2023-09-05T15:01:12Z","abstract":[{"lang":"eng","text":"Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern."}],"type":"book_chapter","month":"10","oa_version":"Submitted Version","volume":68,"file_date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-04T16:20:19Z","year":"2019","_id":"6987"},{"doi":"10.1016/j.it.2019.08.004","quality_controlled":"1","publication_identifier":{"issn":["1471-4906"]},"isi":1,"issue":"10","language":[{"iso":"eng"}],"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"747687"}],"title":"Platelets in host defense: Experimental and clinical insights","author":[{"last_name":"Nicolai","first_name":"Leo","full_name":"Nicolai, Leo"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","last_name":"Gärtner","first_name":"Florian R"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"}],"day":"01","publication":"Trends in Immunology","article_type":"review","article_processing_charge":"No","ec_funded":1,"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Cell Press","department":[{"_id":"MiSi"}],"pmid":1,"date_published":"2019-10-01T00:00:00Z","publication_status":"published","intvolume":"        40","citation":{"ista":"Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 40(10), 922–938.","mla":"Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical Insights.” <i>Trends in Immunology</i>, vol. 40, no. 10, Cell Press, 2019, pp. 922–38, doi:<a href=\"https://doi.org/10.1016/j.it.2019.08.004\">10.1016/j.it.2019.08.004</a>.","apa":"Nicolai, L., Gärtner, F. R., &#38; Massberg, S. (2019). Platelets in host defense: Experimental and clinical insights. <i>Trends in Immunology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.it.2019.08.004\">https://doi.org/10.1016/j.it.2019.08.004</a>","ama":"Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental and clinical insights. <i>Trends in Immunology</i>. 2019;40(10):922-938. doi:<a href=\"https://doi.org/10.1016/j.it.2019.08.004\">10.1016/j.it.2019.08.004</a>","short":"L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938.","ieee":"L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental and clinical insights,” <i>Trends in Immunology</i>, vol. 40, no. 10. Cell Press, pp. 922–938, 2019.","chicago":"Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host Defense: Experimental and Clinical Insights.” <i>Trends in Immunology</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.it.2019.08.004\">https://doi.org/10.1016/j.it.2019.08.004</a>."},"external_id":{"isi":["000493292100005"],"pmid":["31601520"]},"status":"public","volume":40,"date_created":"2019-11-04T16:27:36Z","page":"922-938","month":"10","oa_version":"None","type":"journal_article","date_updated":"2023-08-30T07:19:23Z","abstract":[{"lang":"eng","text":"Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth."}],"_id":"6988","year":"2019"},{"article_processing_charge":"No","scopus_import":"1","publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","department":[{"_id":"HeEd"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"Canadian Conference on Computational Geometry","title":"Folding polyominoes with holes into a cube","arxiv":1,"day":"01","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"full_name":"Akitaya, Hugo A","first_name":"Hugo A","last_name":"Akitaya"},{"last_name":"Cheung","first_name":"Kenneth C","full_name":"Cheung, Kenneth C"},{"full_name":"Demaine, Erik D","last_name":"Demaine","first_name":"Erik D"},{"full_name":"Demaine, Martin L","last_name":"Demaine","first_name":"Martin L"},{"full_name":"Fekete, Sandor P","last_name":"Fekete","first_name":"Sandor P"},{"first_name":"Linda","last_name":"Kleist","full_name":"Kleist, Linda"},{"first_name":"Irina","last_name":"Kostitsyna","full_name":"Kostitsyna, Irina"},{"first_name":"Maarten","last_name":"Löffler","full_name":"Löffler, Maarten"},{"full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová"},{"full_name":"Mundilova, Klara","first_name":"Klara","last_name":"Mundilova"},{"first_name":"Christiane","last_name":"Schmidt","full_name":"Schmidt, Christiane"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2019-08-08","location":"Edmonton, Canada","name":"CCCG: Canadian Conference in Computational Geometry","end_date":"2019-08-10"},"quality_controlled":"1","_id":"6989","year":"2019","acknowledgement":"This research was performed in part at the 33rd BellairsWinter  Workshop  on  Computational  Geometry.    Wethank all other participants for a fruitful atmosphere.","date_created":"2019-11-04T16:46:11Z","type":"conference","oa_version":"Published Version","month":"08","date_updated":"2023-08-04T10:57:42Z","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. "}],"page":"164-170","citation":{"short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170.","chicago":"Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>, 164–70. Canadian Conference on Computational Geometry, 2019.","ieee":"O. Aichholzer <i>et al.</i>, “Folding polyominoes with holes into a cube,” in <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>, Edmonton, Canada, 2019, pp. 164–170.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i> (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.","mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>, Canadian Conference on Computational Geometry, 2019, pp. 164–70.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170.","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>. Canadian Conference on Computational Geometry; 2019:164-170."},"related_material":{"record":[{"relation":"extended_version","id":"8317","status":"public"}]},"external_id":{"arxiv":["1910.09917"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://cccg.ca/proceedings/2019/proceedings.pdf"}],"date_published":"2019-08-01T00:00:00Z","publication_status":"published","oa":1},{"year":"2019","_id":"6999","oa_version":"Published Version","type":"journal_article","month":"10","date_updated":"2023-10-17T12:32:37Z","abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading."}],"page":"21274-21284","date_created":"2019-11-12T11:42:05Z","file_date_updated":"2020-07-14T12:47:46Z","volume":116,"status":"public","external_id":{"pmid":["31575745"],"isi":["000490183000068"]},"citation":{"apa":"Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1911892116\">https://doi.org/10.1073/pnas.1911892116</a>","ista":"Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21274–21284.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:<a href=\"https://doi.org/10.1073/pnas.1911892116\">10.1073/pnas.1911892116</a>.","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2019;116(42):21274-21284. doi:<a href=\"https://doi.org/10.1073/pnas.1911892116\">10.1073/pnas.1911892116</a>","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284.","chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1911892116\">https://doi.org/10.1073/pnas.1911892116</a>.","ieee":"D. Huang <i>et al.</i>, “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 42. Proceedings of the National Academy of Sciences, pp. 21274–21284, 2019."},"intvolume":"       116","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2004738117"}]},"has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2019-10-15T00:00:00Z","ddc":["580"],"department":[{"_id":"JiFr"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Proceedings of the National Academy of Sciences","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences of the United States of America","file":[{"date_updated":"2020-07-14T12:47:46Z","file_id":"7012","checksum":"258c666bc6253eab81961f61169eefae","date_created":"2019-11-13T08:22:28Z","access_level":"open_access","file_name":"2019_PNAS_Huang.pdf","content_type":"application/pdf","relation":"main_file","file_size":3287466,"creator":"dernst"}],"day":"15","author":[{"full_name":"Huang, D","last_name":"Huang","first_name":"D"},{"first_name":"Y","last_name":"Sun","full_name":"Sun, Y"},{"full_name":"Ma, Z","last_name":"Ma","first_name":"Z"},{"full_name":"Ke, M","first_name":"M","last_name":"Ke"},{"last_name":"Cui","first_name":"Y","full_name":"Cui, Y"},{"full_name":"Chen, Z","first_name":"Z","last_name":"Chen"},{"first_name":"C","last_name":"Chen","full_name":"Chen, C"},{"first_name":"C","last_name":"Ji","full_name":"Ji, C"},{"full_name":"Tran, TM","first_name":"TM","last_name":"Tran"},{"full_name":"Yang, L","first_name":"L","last_name":"Yang"},{"full_name":"Lam, SM","first_name":"SM","last_name":"Lam"},{"first_name":"Y","last_name":"Han","full_name":"Han, Y"},{"first_name":"G","last_name":"Shu","full_name":"Shu, G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"full_name":"Miao, Y","last_name":"Miao","first_name":"Y"},{"first_name":"L","last_name":"Jiang","full_name":"Jiang, L"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","issue":"42","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","doi":"10.1073/pnas.1911892116"},{"year":"2019","_id":"7000","month":"12","oa_version":"Published Version","type":"journal_article","date_updated":"2023-08-30T07:20:32Z","abstract":[{"lang":"eng","text":"The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps."}],"date_created":"2019-11-12T12:41:44Z","volume":38,"status":"public","external_id":{"arxiv":["2101.09081"],"isi":["000488973100005"]},"citation":{"apa":"Shehu, Y., Iyiola, O. S., Li, X.-H., &#38; Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. <i>Computational and Applied Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40314-019-0955-9\">https://doi.org/10.1007/s40314-019-0955-9</a>","ista":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 38(4), 161.","mla":"Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” <i>Computational and Applied Mathematics</i>, vol. 38, no. 4, 161, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1007/s40314-019-0955-9\">10.1007/s40314-019-0955-9</a>.","ama":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. <i>Computational and Applied Mathematics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1007/s40314-019-0955-9\">10.1007/s40314-019-0955-9</a>","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” <i>Computational and Applied Mathematics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s40314-019-0955-9\">https://doi.org/10.1007/s40314-019-0955-9</a>.","ieee":"Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” <i>Computational and Applied Mathematics</i>, vol. 38, no. 4. Springer Nature, 2019."},"intvolume":"        38","has_accepted_license":"1","publication_status":"published","oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"ddc":["510","515","518"],"date_published":"2019-12-01T00:00:00Z","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","article_processing_charge":"No","scopus_import":"1","ec_funded":1,"publication":"Computational and Applied Mathematics","day":"01","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini","last_name":"Shehu"},{"full_name":"Iyiola, Olaniyi S.","first_name":"Olaniyi S.","last_name":"Iyiola"},{"last_name":"Li","first_name":"Xiao-Huan","full_name":"Li, Xiao-Huan"},{"full_name":"Dong, Qiao-Li","last_name":"Dong","first_name":"Qiao-Li"}],"article_number":"161","arxiv":1,"title":"Convergence analysis of projection method for variational inequalities","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"issue":"4","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"eissn":["1807-0302"],"issn":["2238-3603"]},"quality_controlled":"1","doi":"10.1007/s40314-019-0955-9"},{"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"}],"issue":"4","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"quality_controlled":"1","doi":"10.1016/j.cell.2019.10.006","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"pmid":1,"publisher":"Cell Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","ec_funded":1,"scopus_import":"1","article_processing_charge":"No","publication":"Cell","day":"31","file":[{"creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":8805878,"success":1,"file_name":"2019_Cell_Schwayer_accepted.pdf","access_level":"open_access","date_created":"2020-10-21T07:09:45Z","checksum":"33dac4bb77ee630e2666e936b4d57980","date_updated":"2020-10-21T07:09:45Z","file_id":"8684"}],"author":[{"full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","first_name":"Cornelia"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"last_name":"Pranjic-Ferscha","first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","first_name":"Alexandra"},{"full_name":"Balda, M","last_name":"Balda","first_name":"M"},{"full_name":"Tada, M","first_name":"M","last_name":"Tada"},{"first_name":"K","last_name":"Matter","full_name":"Matter, K"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","status":"public","external_id":{"pmid":["31675500"],"isi":["000493898000012"]},"citation":{"apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>.","ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019."},"related_material":{"record":[{"relation":"dissertation_contains","id":"7186","status":"public"},{"relation":"dissertation_contains","id":"8350","status":"public"}],"link":[{"relation":"press_release","description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/"}]},"intvolume":"       179","has_accepted_license":"1","publication_status":"published","oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"date_published":"2019-10-31T00:00:00Z","ddc":["570"],"year":"2019","_id":"7001","type":"journal_article","month":"10","oa_version":"Submitted Version","date_updated":"2024-03-25T23:30:21Z","page":"937-952.e18","date_created":"2019-11-12T12:51:06Z","file_date_updated":"2020-10-21T07:09:45Z","volume":179},{"issue":"4","language":[{"iso":"eng"}],"isi":1,"project":[{"name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"}],"quality_controlled":"1","doi":"10.1145/3306346.3323009","publication_identifier":{"issn":["0730-0301"]},"article_type":"original","scopus_import":"1","ec_funded":1,"article_processing_charge":"No","publication":"ACM Transactions on Graphics","department":[{"_id":"ChWo"}],"publisher":"ACM","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"37","title":"Optimal multiple importance sampling","day":"01","author":[{"first_name":"Ivo","last_name":"Kondapaneni","full_name":"Kondapaneni, Ivo"},{"full_name":"Vevoda, Petr","first_name":"Petr","last_name":"Vevoda"},{"first_name":"Pascal","last_name":"Grittmann","full_name":"Grittmann, Pascal"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas","last_name":"Skrivan","first_name":"Tomas"},{"last_name":"Slusallek","first_name":"Philipp","full_name":"Slusallek, Philipp"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"}],"citation":{"short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019).","chicago":"Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3323009\">https://doi.org/10.1145/3306346.3323009</a>.","ieee":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","apa":"Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., &#38; Křivánek, J. (2019). Optimal multiple importance sampling. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3323009\">https://doi.org/10.1145/3306346.3323009</a>","ista":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. 2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4), 37.","mla":"Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 37, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3323009\">10.1145/3306346.3323009</a>.","ama":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3323009\">10.1145/3306346.3323009</a>"},"intvolume":"        38","status":"public","external_id":{"isi":["000475740600011"]},"date_published":"2019-07-01T00:00:00Z","publication_status":"published","_id":"7002","year":"2019","date_created":"2019-11-12T13:05:40Z","volume":38,"type":"journal_article","month":"07","oa_version":"None","date_updated":"2023-08-30T07:21:25Z","abstract":[{"lang":"eng","text":"Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem."}]},{"date_created":"2019-11-12T14:37:08Z","file_date_updated":"2020-07-14T12:47:47Z","volume":151,"oa_version":"Published Version","type":"journal_article","month":"12","abstract":[{"text":"Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes.","lang":"eng"}],"date_updated":"2023-08-30T07:21:50Z","page":"570-583","_id":"7005","year":"2019","ddc":["570"],"date_published":"2019-12-01T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"ama":"Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. <i>Journal of Neurochemistry</i>. 2019;151(5):570-583. doi:<a href=\"https://doi.org/10.1111/jnc.14862\">10.1111/jnc.14862</a>","apa":"Cheung, G. T., &#38; Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. <i>Journal of Neurochemistry</i>. Wiley. <a href=\"https://doi.org/10.1111/jnc.14862\">https://doi.org/10.1111/jnc.14862</a>","ista":"Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 151(5), 570–583.","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” <i>Journal of Neurochemistry</i>, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:<a href=\"https://doi.org/10.1111/jnc.14862\">10.1111/jnc.14862</a>.","chicago":"Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” <i>Journal of Neurochemistry</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/jnc.14862\">https://doi.org/10.1111/jnc.14862</a>.","ieee":"G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” <i>Journal of Neurochemistry</i>, vol. 151, no. 5. Wiley, pp. 570–583, 2019.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583."},"intvolume":"       151","status":"public","external_id":{"isi":["000490703100001"],"pmid":["31479508"]},"title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","day":"01","file":[{"file_size":4334962,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2019_JournNeurochemistry_Cheung.pdf","date_created":"2020-02-05T10:30:02Z","access_level":"open_access","file_id":"7452","date_updated":"2020-07-14T12:47:47Z","checksum":"ec1fb2aebb874009bc309adaada6e1d7"}],"author":[{"orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung"},{"full_name":"Cousin, Michael A.","last_name":"Cousin","first_name":"Michael A."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"No","scopus_import":"1","publication":"Journal of Neurochemistry","department":[{"_id":"SiHi"}],"pmid":1,"publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","doi":"10.1111/jnc.14862","publication_identifier":{"issn":["0022-3042"],"eissn":["1471-4159"]},"issue":"5","language":[{"iso":"eng"}],"isi":1},{"issue":"10","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1999-4893"]},"doi":"10.3390/a12100218","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"MDPI","department":[{"_id":"MaMo"}],"publication":"Algorithms","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":1,"author":[{"last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020"},{"first_name":"S. Hamed","last_name":"Hassani","full_name":"Hassani, S. Hamed"},{"first_name":"Rüdiger","last_name":"Urbanke","full_name":"Urbanke, Rüdiger"}],"file":[{"file_name":"2019_Algorithms_Mondelli.pdf","relation":"main_file","content_type":"application/pdf","file_size":696791,"creator":"dernst","date_updated":"2020-07-14T12:47:47Z","file_id":"7008","checksum":"267756d8f9db572f496cd1663c89d59a","date_created":"2019-11-12T14:48:45Z","access_level":"open_access"}],"day":"18","article_number":"218","arxiv":1,"title":"A new coding paradigm for the primitive relay channel","external_id":{"arxiv":["1801.03153"]},"status":"public","intvolume":"        12","related_material":{"record":[{"id":"6675","status":"public","relation":"earlier_version"}]},"citation":{"mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” <i>Algorithms</i>, vol. 12, no. 10, 218, MDPI, 2019, doi:<a href=\"https://doi.org/10.3390/a12100218\">10.3390/a12100218</a>.","ista":"Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218.","apa":"Mondelli, M., Hassani, S. H., &#38; Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. <i>Algorithms</i>. MDPI. <a href=\"https://doi.org/10.3390/a12100218\">https://doi.org/10.3390/a12100218</a>","ama":"Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. <i>Algorithms</i>. 2019;12(10). doi:<a href=\"https://doi.org/10.3390/a12100218\">10.3390/a12100218</a>","short":"M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).","ieee":"M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” <i>Algorithms</i>, vol. 12, no. 10. MDPI, 2019.","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” <i>Algorithms</i>. MDPI, 2019. <a href=\"https://doi.org/10.3390/a12100218\">https://doi.org/10.3390/a12100218</a>."},"oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2019-10-18T00:00:00Z","ddc":["510"],"year":"2019","_id":"7007","oa_version":"Published Version","month":"10","type":"journal_article","date_updated":"2023-02-23T12:49:28Z","abstract":[{"text":"We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds.","lang":"eng"}],"volume":12,"file_date_updated":"2020-07-14T12:47:47Z","date_created":"2019-11-12T14:46:19Z"},{"page":"738–752","type":"journal_article","oa_version":"None","month":"12","date_updated":"2023-08-30T07:22:20Z","abstract":[{"lang":"eng","text":"Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration."}],"volume":20,"date_created":"2019-11-12T14:54:42Z","year":"2019","_id":"7009","publication_status":"published","date_published":"2019-12-01T00:00:00Z","external_id":{"pmid":["31582855"],"isi":["000497966900007"]},"status":"public","intvolume":"        20","citation":{"short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.","ieee":"K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.","chicago":"Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41580-019-0172-9\">https://doi.org/10.1038/s41580-019-0172-9</a>.","ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752.","mla":"Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:<a href=\"https://doi.org/10.1038/s41580-019-0172-9\">10.1038/s41580-019-0172-9</a>.","apa":"Yamada, K., &#38; Sixt, M. K. (2019). Mechanisms of 3D cell migration. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41580-019-0172-9\">https://doi.org/10.1038/s41580-019-0172-9</a>","ama":"Yamada K, Sixt MK. Mechanisms of 3D cell migration. <i>Nature Reviews Molecular Cell Biology</i>. 2019;20(12):738–752. doi:<a href=\"https://doi.org/10.1038/s41580-019-0172-9\">10.1038/s41580-019-0172-9</a>"},"author":[{"full_name":"Yamada, KM","first_name":"KM","last_name":"Yamada"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"day":"01","title":"Mechanisms of 3D cell migration","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiSi"}],"pmid":1,"publication":"Nature Reviews Molecular Cell Biology","article_type":"review","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"doi":"10.1038/s41580-019-0172-9","quality_controlled":"1","isi":1,"issue":"12","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"conference":{"end_date":"2019-06-27","start_date":"2019-06-26","location":"Munich, Germany","name":"European Conferences on Biomedical Optics"},"isi":1,"quality_controlled":"1","doi":"10.1117/12.2527058","publication_identifier":{"isbn":["9781510628458"],"issn":["1605-7422"]},"scopus_import":"1","article_processing_charge":"No","publication":"Advances in Microscopic Imaging II","department":[{"_id":"MaLo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"SPIE","article_number":"110760V","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","day":"22","author":[{"full_name":"Davies, Heather S.","first_name":"Heather S.","last_name":"Davies"},{"first_name":"Natalia S.","last_name":"Baranova","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"last_name":"El Amri","first_name":"Nouha","full_name":"El Amri, Nouha"},{"full_name":"Coche-Guérente, Liliane","first_name":"Liliane","last_name":"Coche-Guérente"},{"full_name":"Verdier, Claude","first_name":"Claude","last_name":"Verdier"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"full_name":"Richter, Ralf P.","first_name":"Ralf P.","last_name":"Richter"},{"full_name":"Débarre, Delphine","first_name":"Delphine","last_name":"Débarre"}],"citation":{"ama":"Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: <i>Advances in Microscopic Imaging II</i>. Vol 11076. SPIE; 2019. doi:<a href=\"https://doi.org/10.1117/12.2527058\">10.1117/12.2527058</a>","mla":"Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” <i>Advances in Microscopic Imaging II</i>, vol. 11076, 110760V, SPIE, 2019, doi:<a href=\"https://doi.org/10.1117/12.2527058\">10.1117/12.2527058</a>.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. Advances in Microscopic Imaging II. European Conferences on Biomedical Optics vol. 11076, 110760V.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In <i>Advances in Microscopic Imaging II</i> (Vol. 11076). Munich, Germany: SPIE. <a href=\"https://doi.org/10.1117/12.2527058\">https://doi.org/10.1117/12.2527058</a>","ieee":"H. S. Davies <i>et al.</i>, “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in <i>Advances in Microscopic Imaging II</i>, Munich, Germany, 2019, vol. 11076.","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In <i>Advances in Microscopic Imaging II</i>, Vol. 11076. SPIE, 2019. <a href=\"https://doi.org/10.1117/12.2527058\">https://doi.org/10.1117/12.2527058</a>.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE, 2019."},"intvolume":"     11076","status":"public","external_id":{"isi":["000535353000023"]},"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf","open_access":"1"}],"date_published":"2019-07-22T00:00:00Z","publication_status":"published","oa":1,"_id":"7010","year":"2019","date_created":"2019-11-12T15:10:18Z","volume":11076,"oa_version":"Published Version","month":"07","type":"conference","abstract":[{"lang":"eng","text":"Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines."}],"date_updated":"2023-08-29T06:54:38Z"},{"volume":100,"date_created":"2019-11-13T08:25:48Z","date_updated":"2024-02-28T13:13:13Z","abstract":[{"lang":"eng","text":"Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition."}],"month":"10","type":"journal_article","oa_version":"Preprint","_id":"7013","year":"2019","date_published":"2019-10-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"publication_status":"published","oa":1,"intvolume":"       100","citation":{"apa":"Orell, T., Michailidis, A., Serbyn, M., &#38; Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.100.134504\">https://doi.org/10.1103/physrevb.100.134504</a>","ista":"Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 100(13), 134504.","mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” <i>Physical Review B</i>, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.100.134504\">10.1103/physrevb.100.134504</a>.","ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. <i>Physical Review B</i>. 2019;100(13). doi:<a href=\"https://doi.org/10.1103/physrevb.100.134504\">10.1103/physrevb.100.134504</a>","short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).","chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.100.134504\">https://doi.org/10.1103/physrevb.100.134504</a>.","ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” <i>Physical Review B</i>, vol. 100, no. 13. American Physical Society, 2019."},"status":"public","external_id":{"arxiv":["1907.04043"],"isi":["000489036500004"]},"arxiv":1,"title":"Probing the many-body localization phase transition with superconducting circuits","article_number":"134504","author":[{"last_name":"Orell","first_name":"Tuure","full_name":"Orell, Tuure"},{"full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","last_name":"Michailidis","first_name":"Alexios"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Silveri, Matti","last_name":"Silveri","first_name":"Matti"}],"day":"01","publication":"Physical Review B","article_processing_charge":"No","scopus_import":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"doi":"10.1103/physrevb.100.134504","quality_controlled":"1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"isi":1,"language":[{"iso":"eng"}],"issue":"13"},{"publisher":"ACM","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KrCh"}],"publication":"ACM Transactions on Programming Languages and Systems","article_type":"original","ec_funded":1,"article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady"}],"day":"01","article_number":"20","arxiv":1,"title":"Non-polynomial worst-case analysis of recursive programs","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"isi":1,"issue":"4","language":[{"iso":"eng"}],"doi":"10.1145/3339984","quality_controlled":"1","year":"2019","_id":"7014","type":"journal_article","month":"10","oa_version":"Preprint","date_updated":"2025-06-02T08:53:47Z","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms."}],"volume":41,"date_created":"2019-11-13T08:33:43Z","status":"public","external_id":{"isi":["000564108400001"],"arxiv":["1705.00317"]},"related_material":{"record":[{"status":"public","id":"639","relation":"earlier_version"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"intvolume":"        41","citation":{"apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. <i>ACM Transactions on Programming Languages and Systems</i>. ACM. <a href=\"https://doi.org/10.1145/3339984\">https://doi.org/10.1145/3339984</a>","mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4, 20, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3339984\">10.1145/3339984</a>.","ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. <i>ACM Transactions on Programming Languages and Systems</i>. 2019;41(4). doi:<a href=\"https://doi.org/10.1145/3339984\">10.1145/3339984</a>","short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019).","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” <i>ACM Transactions on Programming Languages and Systems</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3339984\">https://doi.org/10.1145/3339984</a>.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4. ACM, 2019."},"oa":1,"publication_status":"published","date_published":"2019-10-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1705.00317","open_access":"1"}]},{"volume":100,"date_created":"2019-11-13T08:41:48Z","abstract":[{"text":"We modify the \"floating crystal\" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential.","lang":"eng"}],"date_updated":"2024-02-28T13:13:23Z","month":"07","type":"journal_article","oa_version":"Preprint","_id":"7015","year":"2019","date_published":"2019-07-25T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1905.09138","open_access":"1"}],"oa":1,"publication_status":"published","intvolume":"       100","citation":{"ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” <i>Physical Review B</i>, vol. 100, no. 3. American Physical Society, 2019.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.100.035127\">https://doi.org/10.1103/physrevb.100.035127</a>.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).","ama":"Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. <i>Physical Review B</i>. 2019;100(3). doi:<a href=\"https://doi.org/10.1103/physrevb.100.035127\">10.1103/physrevb.100.035127</a>","mla":"Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” <i>Physical Review B</i>, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.100.035127\">10.1103/physrevb.100.035127</a>.","ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127.","apa":"Lewin, M., Lieb, E. H., &#38; Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.100.035127\">https://doi.org/10.1103/physrevb.100.035127</a>"},"external_id":{"arxiv":["1905.09138"],"isi":["000477888200001"]},"status":"public","arxiv":1,"title":"Floating Wigner crystal with no boundary charge fluctuations","article_number":"035127","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"first_name":"Elliott H.","last_name":"Lieb","full_name":"Lieb, Elliott H."},{"first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"day":"25","publication":"Physical Review B","scopus_import":"1","ec_funded":1,"article_processing_charge":"No","article_type":"original","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"doi":"10.1103/physrevb.100.035127","quality_controlled":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"isi":1,"language":[{"iso":"eng"}],"issue":"3","project":[{"grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"}]},{"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","department":[{"_id":"CaGu"}],"_id":"7016","article_processing_charge":"No","author":[{"full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","last_name":"Tomanek","first_name":"Isabella"}],"file":[{"creator":"itomanek","content_type":"application/octet-stream","relation":"main_file","file_size":2456192500,"file_name":"D8_S35_R2_001.fastq","access_level":"open_access","title":"Locus1_amplified","date_created":"2019-11-13T08:52:21Z","description":"Illumina whole genome sequence data for Locus 1 - amplified.","checksum":"72441055043eda4cbf1398a422e2c118","date_updated":"2020-07-14T12:47:47Z","file_id":"7017"},{"date_updated":"2020-07-14T12:47:47Z","file_id":"7018","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","description":"Illumina whole genome sequence data for Locus 1 - ancestral.","date_created":"2019-11-13T08:52:59Z","access_level":"open_access","title":"Locus1_ancestral","file_name":"IT028_S11_R2_001.fastq","relation":"main_file","content_type":"application/octet-stream","file_size":2833452234,"creator":"itomanek"},{"date_updated":"2020-07-14T12:47:47Z","file_id":"7019","description":"Illumina whole genome sequence data for Locus 1 - amplified, after DOG-selection.","checksum":"5b227708ff478ca06e3f0448a4efdc2f","date_created":"2019-11-13T08:54:10Z","title":"Locus1_amplified_DOG","access_level":"open_access","file_name":"D8-DOG1_S47_R2_001.fastq","content_type":"application/octet-stream","relation":"main_file","file_size":2878017264,"creator":"itomanek"},{"date_created":"2019-11-13T08:54:27Z","access_level":"open_access","title":"Locus2_amplified","file_id":"7020","date_updated":"2020-07-14T12:47:47Z","checksum":"d9550a4c044116075fa83f8f2ea31d6f","description":"Illumina whole genome sequence data for Locus 2 - amplified.","file_size":2180826995,"relation":"main_file","content_type":"application/octet-stream","creator":"itomanek","file_name":"D4_S71_R2_001.fastq"},{"file_size":2108826444,"relation":"main_file","content_type":"application/octet-stream","creator":"itomanek","file_name":"IT030_S23_R2_001.fastq","date_created":"2019-11-13T08:55:58Z","title":"Locus2_ancestral","access_level":"open_access","file_id":"7021","date_updated":"2020-07-14T12:47:47Z","description":"Illumina whole genome sequence data for Locus 2 - ancestral.","checksum":"466ceb302c020ac013007a879fcde69d"},{"checksum":"8aeb1da771713c7baa5a847eff889604","description":"Illumina whole genome sequence data for Locus 2 - amplified, after DOG-selection.","date_updated":"2020-07-14T12:47:47Z","file_id":"7092","title":"Locus2_amplified_DOG","access_level":"open_access","date_created":"2019-11-21T12:31:01Z","file_name":"D4-DOG1_S83_R2_001.fastq","creator":"itomanek","relation":"main_file","content_type":"application/octet-stream","file_size":3144330494},{"date_created":"2020-01-14T11:22:27Z","access_level":"open_access","title":"DNA sequence of the chromosomal reporter gene cassette","date_updated":"2020-07-14T12:47:47Z","file_id":"7273","checksum":"bf7d4b053f14af4655fb5574209fdb2d","description":"Compressed genbank file format containing the sequence of the chromosomal reporter gene cassette.","content_type":"application/zip","relation":"main_file","file_size":4179,"creator":"itomanek","file_name":"galK_dual_reporter_cassette.gb.zip"},{"creator":"dernst","file_size":435,"content_type":"text/plain","relation":"main_file","file_name":"Readme_7016.txt","access_level":"open_access","title":"Read_me_sequence_data","date_created":"2020-01-15T14:15:55Z","checksum":"5e91cee2eff6f4a7cde456c6fb07c2ff","file_id":"7335","date_updated":"2020-07-14T12:47:47Z"},{"creator":"itomanek","relation":"main_file","content_type":"application/zip","file_size":3765861,"file_name":"FACS_data.xlsx.zip","title":"FACS data","access_level":"open_access","date_created":"2020-01-22T15:44:16Z","checksum":"5e6745dcfb9c1b11dd935ac3ee45fe33","description":"FACS data associated with Fig. 2c - see read_me_FACS","date_updated":"2020-07-14T12:47:47Z","file_id":"7351"},{"creator":"itomanek","content_type":"text/rtf","relation":"main_file","file_size":4996,"file_name":"read_me_FACS.rtf","access_level":"open_access","date_created":"2020-01-22T15:44:16Z","checksum":"a85caf092ae4b17668f70af2d93fad00","date_updated":"2020-07-14T12:47:47Z","file_id":"7352"},{"file_name":"read_me_microfluidics.rtf","creator":"itomanek","file_size":868,"relation":"main_file","content_type":"text/rtf","checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","file_id":"7353","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","date_created":"2020-01-22T15:44:16Z"},{"creator":"itomanek","content_type":"application/zip","relation":"main_file","file_size":8141727,"file_name":"microfuidics_data.zip","title":"microfluidics data","access_level":"open_access","date_created":"2020-01-22T15:44:17Z","checksum":"69c5dc5ca5c069a138183c934acc1778","description":"microfluidics time trace data - see read_me_microfluidics","date_updated":"2020-07-14T12:47:47Z","file_id":"7354"}],"day":"13","abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"date_updated":"2024-02-21T12:45:25Z","month":"11","oa_version":"Published Version","type":"research_data","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","date_created":"2019-11-13T09:07:31Z","file_date_updated":"2020-07-14T12:47:47Z","status":"public","related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"citation":{"ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7016\">10.15479/AT:ISTA:7016</a>","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7016\">10.15479/AT:ISTA:7016</a>.","mla":"Tomanek, Isabella. <i>Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.”</i> Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7016\">10.15479/AT:ISTA:7016</a>.","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7016\">https://doi.org/10.15479/AT:ISTA:7016</a>","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7016\">https://doi.org/10.15479/AT:ISTA:7016</a>.","short":"I. Tomanek, (2019)."},"oa":1,"has_accepted_license":"1","ddc":["576"],"doi":"10.15479/AT:ISTA:7016","date_published":"2019-11-13T00:00:00Z","contributor":[{"last_name":"Guet","contributor_type":"project_leader","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}]},{"volume":9,"file_date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-15T10:51:42Z","page":"423-433.e1-e3","type":"journal_article","oa_version":"Published Version","month":"11","abstract":[{"text":"Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information.","lang":"eng"}],"date_updated":"2023-08-30T07:24:58Z","_id":"7026","year":"2019","ddc":["570"],"date_published":"2019-11-27T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"}],"oa":1,"publication_status":"published","has_accepted_license":"1","intvolume":"         9","citation":{"ieee":"M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” <i>Cell Systems</i>, vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019.","chicago":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” <i>Cell Systems</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">https://doi.org/10.1016/j.cels.2019.10.004</a>.","short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.","ama":"Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. <i>Cell Systems</i>. 2019;9(5):423-433.e1-e3. doi:<a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">10.1016/j.cels.2019.10.004</a>","mla":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” <i>Cell Systems</i>, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:<a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">10.1016/j.cels.2019.10.004</a>.","ista":"Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3.","apa":"Lukacisin, M., &#38; Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2019.10.004\">https://doi.org/10.1016/j.cels.2019.10.004</a>"},"external_id":{"isi":["000499495400003"]},"status":"public","title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","author":[{"last_name":"Lukacisin","first_name":"Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin"},{"first_name":"Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"}],"day":"27","file":[{"file_size":4238460,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2019_CellSystems_Lukacisin.pdf","date_created":"2019-11-15T10:57:42Z","access_level":"open_access","file_id":"7027","date_updated":"2020-07-14T12:47:48Z","checksum":"7a11d6c2f9523d65b049512d61733178"}],"publication":"Cell Systems","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","publisher":"Cell Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToBo"}],"doi":"10.1016/j.cels.2019.10.004","quality_controlled":"1","publication_identifier":{"issn":["2405-4712"]},"isi":1,"issue":"5","language":[{"iso":"eng"}],"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}]}]