--- _id: '6982' 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" article_number: '50' article_type: original arxiv: 1 author: - first_name: Hugo full_name: Akitaya, Hugo last_name: Akitaya - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Csaba full_name: Tóth, Csaba last_name: Tóth citation: ama: Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 2019;15(4). doi:10.1145/3344549 apa: Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549 chicago: Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549. ieee: H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019. 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.” ACM Transactions on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549. short: H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019). date_created: 2019-11-04T15:45:17Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-09-15T12:19:31Z day: '01' department: - _id: UlWa doi: 10.1145/3344549 external_id: arxiv: - '1709.09209' intvolume: ' 15' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.09209 month: '10' oa: 1 oa_version: Preprint project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: ACM Transactions on Algorithms publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '309' relation: earlier_version status: public scopus_import: 1 status: public title: Recognizing weak embeddings of graphs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2019' ... --- _id: '6983' abstract: - lang: eng 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. article_number: '2153' article_processing_charge: No article_type: original author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 - first_name: H full_name: Rajakaruna, H last_name: Rajakaruna - first_name: IA full_name: Cockburn, IA last_name: Cockburn - first_name: VV full_name: Ganusov, VV last_name: Ganusov citation: 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. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153 apa: Kelemen, R. K., 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. Frontiers. https://doi.org/10.3389/fimmu.2019.02153 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.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153. 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,” Frontiers in Immunology, vol. 10. Frontiers, 2019. 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.” Frontiers in Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153. short: R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019). date_created: 2019-11-04T15:50:06Z date_published: 2019-09-20T00:00:00Z date_updated: 2023-08-30T07:18:23Z day: '20' ddc: - '570' department: - _id: BeVi doi: 10.3389/fimmu.2019.02153 external_id: isi: - '000487187000001' pmid: - '31616407' file: - access_level: open_access checksum: 68d1708f7aa412544159b498ef17a6b9 content_type: application/pdf creator: dernst date_created: 2019-11-04T15:54:00Z date_updated: 2020-07-14T12:47:46Z file_id: '6984' file_name: 2019_FrontiersImmonology_Kelemen.pdf file_size: 2083061 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Immunology publication_identifier: issn: - 1664-3224 publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6985' abstract: - lang: eng 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. article_number: '8851954' arxiv: 1 author: - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Felix full_name: Naser, Felix last_name: Naser - first_name: Radu full_name: Grosu, Radu last_name: Grosu - first_name: Daniela full_name: Rus, Daniela last_name: Rus citation: 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: Proceedings of the International Joint Conference on Neural Networks. IEEE; 2019. doi:10.1109/ijcnn.2019.8851954' apa: '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. In Proceedings of the International Joint Conference on Neural Networks. Budapest, Hungary: IEEE. https://doi.org/10.1109/ijcnn.2019.8851954' 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 Proceedings of the International Joint Conference on Neural Networks. IEEE, 2019. https://doi.org/10.1109/ijcnn.2019.8851954. 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 Proceedings of the International Joint Conference on Neural Networks, Budapest, Hungary, 2019. 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.' mla: Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” Proceedings of the International Joint Conference on Neural Networks, 8851954, IEEE, 2019, doi:10.1109/ijcnn.2019.8851954. 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. conference: end_date: 2019-07-19 location: Budapest, Hungary name: 'IJCNN: International Joint Conference on Neural Networks' start_date: 2019-07-14 date_created: 2019-11-04T15:59:58Z date_published: 2019-09-30T00:00:00Z date_updated: 2021-01-12T08:11:19Z day: '30' department: - _id: ToHe doi: 10.1109/ijcnn.2019.8851954 external_id: arxiv: - '1809.03864' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.03864 month: '09' oa: 1 oa_version: Preprint publication: Proceedings of the International Joint Conference on Neural Networks publication_identifier: isbn: - '9781728119854' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: 1 status: public title: Response characterization for auditing cell dynamics in long short-term memory networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6986' 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. ' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Penghui full_name: Li, Penghui id: 42A24CCC-F248-11E8-B48F-1D18A9856A87 last_name: Li citation: ama: Li P. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586 apa: Li, P. (2019). A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586 chicago: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586. ieee: P. Li, “A colimit of traces of reflection groups,” Proceedings of the American Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019. ista: Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604. mla: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604, doi:10.1090/proc/14586. short: P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604. date_created: 2019-11-04T16:10:50Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-09-05T12:22:21Z day: '01' department: - _id: TaHa doi: 10.1090/proc/14586 ec_funded: 1 external_id: arxiv: - '1810.07039' isi: - '000488621700004' intvolume: ' 147' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.07039 month: '11' oa: 1 oa_version: Preprint page: 4597-4604 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Proceedings of the American Mathematical Society publication_identifier: eissn: - 1088-6826 issn: - 0002-9939 publication_status: published publisher: AMS quality_controlled: '1' scopus_import: '1' status: public title: A colimit of traces of reflection groups type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 147 year: '2019' ... --- _id: '6987' 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. alternative_title: - RESULTS article_processing_charge: No author: - first_name: Alex full_name: McDougall, Alex last_name: McDougall - first_name: Janet full_name: Chenevert, Janet last_name: Chenevert - first_name: Benoit G full_name: Godard, Benoit G id: 33280250-F248-11E8-B48F-1D18A9856A87 last_name: Godard - first_name: Remi full_name: Dumollard, Remi last_name: Dumollard citation: ama: 'McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154. doi:10.1007/978-3-030-23459-1_6' apa: 'McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski (Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol. 68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6' chicago: 'McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6.' ieee: 'A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.' 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.' mla: 'McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:10.1007/978-3-030-23459-1_6.' 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.' date_created: 2019-11-04T16:20:19Z date_published: 2019-10-10T00:00:00Z date_updated: 2023-09-05T15:01:12Z day: '10' ddc: - '570' department: - _id: CaHe doi: 10.1007/978-3-030-23459-1_6 editor: - first_name: Waclaw full_name: Tworzydlo, Waclaw last_name: Tworzydlo - first_name: Szczepan M. full_name: Bilinski, Szczepan M. last_name: Bilinski external_id: pmid: - '31598855' file: - access_level: open_access checksum: 7f43e1e3706d15061475c5c57efc2786 content_type: application/pdf creator: dernst date_created: 2020-05-14T10:09:30Z date_updated: 2020-07-14T12:47:46Z file_id: '7829' file_name: 2019_RESULTS_McDougall.pdf file_size: 19317348 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 68' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 127-154 pmid: 1 publication: 'Evo-Devo: Non-model species in cell and developmental biology' publication_identifier: eissn: - 1861-0412 isbn: - '9783030234584' - '9783030234591' issn: - 0080-1844 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Emergence of embryo shape during cleavage divisions type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 68 year: '2019' ... --- _id: '6988' 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.' article_processing_charge: No article_type: review author: - first_name: Leo full_name: Nicolai, Leo last_name: Nicolai - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg citation: ama: 'Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004' apa: 'Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host defense: Experimental and clinical insights. Trends in Immunology. Cell Press. https://doi.org/10.1016/j.it.2019.08.004' chicago: 'Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell Press, 2019. https://doi.org/10.1016/j.it.2019.08.004.' ieee: 'L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press, pp. 922–938, 2019.' 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.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp. 922–38, doi:10.1016/j.it.2019.08.004.' short: L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938. date_created: 2019-11-04T16:27:36Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-30T07:19:23Z day: '01' department: - _id: MiSi doi: 10.1016/j.it.2019.08.004 ec_funded: 1 external_id: isi: - '000493292100005' pmid: - '31601520' intvolume: ' 40' isi: 1 issue: '10' language: - iso: eng month: '10' oa_version: None page: 922-938 pmid: 1 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Trends in Immunology publication_identifier: issn: - 1471-4906 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: 'Platelets in host defense: Experimental and clinical insights' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2019' ... --- _id: '6989' 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. ' acknowledgement: This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere. article_processing_charge: No arxiv: 1 author: - first_name: Oswin full_name: Aichholzer, Oswin last_name: Aichholzer - first_name: Hugo A full_name: Akitaya, Hugo A last_name: Akitaya - first_name: Kenneth C full_name: Cheung, Kenneth C last_name: Cheung - first_name: Erik D full_name: Demaine, Erik D last_name: Demaine - first_name: Martin L full_name: Demaine, Martin L last_name: Demaine - first_name: Sandor P full_name: Fekete, Sandor P last_name: Fekete - first_name: Linda full_name: Kleist, Linda last_name: Kleist - first_name: Irina full_name: Kostitsyna, Irina last_name: Kostitsyna - first_name: Maarten full_name: Löffler, Maarten last_name: Löffler - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Klara full_name: Mundilova, Klara last_name: Mundilova - first_name: Christiane full_name: Schmidt, Christiane last_name: Schmidt citation: ama: 'Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.' 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 Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.' 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 Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019. ieee: O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170. 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.' mla: Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70. 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. conference: end_date: 2019-08-10 location: Edmonton, Canada name: 'CCCG: Canadian Conference in Computational Geometry' start_date: 2019-08-08 date_created: 2019-11-04T16:46:11Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-04T10:57:42Z day: '01' department: - _id: HeEd external_id: arxiv: - '1910.09917' language: - iso: eng main_file_link: - open_access: '1' url: https://cccg.ca/proceedings/2019/proceedings.pdf month: '08' oa: 1 oa_version: Published Version page: 164-170 publication: Proceedings of the 31st Canadian Conference on Computational Geometry publication_status: published publisher: Canadian Conference on Computational Geometry quality_controlled: '1' related_material: record: - id: '8317' relation: extended_version status: public scopus_import: '1' status: public title: Folding polyominoes with holes into a cube type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 year: '2019' ... --- _id: '6999' 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. article_processing_charge: No article_type: original author: - first_name: D full_name: Huang, D last_name: Huang - first_name: Y full_name: Sun, Y last_name: Sun - first_name: Z full_name: Ma, Z last_name: Ma - first_name: M full_name: Ke, M last_name: Ke - first_name: Y full_name: Cui, Y last_name: Cui - first_name: Z full_name: Chen, Z last_name: Chen - first_name: C full_name: Chen, C last_name: Chen - first_name: C full_name: Ji, C last_name: Ji - first_name: TM full_name: Tran, TM last_name: Tran - first_name: L full_name: Yang, L last_name: Yang - first_name: SM full_name: Lam, SM last_name: Lam - first_name: Y full_name: Han, Y last_name: Han - first_name: G full_name: Shu, G last_name: Shu - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Y full_name: Miao, Y last_name: Miao - first_name: L full_name: Jiang, L last_name: Jiang - first_name: X full_name: Chen, X last_name: Chen citation: ama: Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116 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. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116 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.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116. ieee: D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42. Proceedings of the National Academy of Sciences, pp. 21274–21284, 2019. 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.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116. 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. date_created: 2019-11-12T11:42:05Z date_published: 2019-10-15T00:00:00Z date_updated: 2023-10-17T12:32:37Z day: '15' ddc: - '580' department: - _id: JiFr doi: 10.1073/pnas.1911892116 external_id: isi: - '000490183000068' pmid: - '31575745' file: - access_level: open_access checksum: 258c666bc6253eab81961f61169eefae content_type: application/pdf creator: dernst date_created: 2019-11-13T08:22:28Z date_updated: 2020-07-14T12:47:46Z file_id: '7012' file_name: 2019_PNAS_Huang.pdf file_size: 3287466 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 116' isi: 1 issue: '42' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 21274-21284 pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1073/pnas.2004738117 scopus_import: '1' status: public title: Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 116 year: '2019' ... --- _id: '7000' 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. article_number: '161' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Olaniyi S. full_name: Iyiola, Olaniyi S. last_name: Iyiola - first_name: Xiao-Huan full_name: Li, Xiao-Huan last_name: Li - first_name: Qiao-Li full_name: Dong, Qiao-Li last_name: Dong citation: ama: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 2019;38(4). doi:10.1007/s40314-019-0955-9 apa: Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9 chicago: Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9. ieee: Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” Computational and Applied Mathematics, vol. 38, no. 4. Springer Nature, 2019. 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.” Computational and Applied Mathematics, vol. 38, no. 4, 161, Springer Nature, 2019, doi:10.1007/s40314-019-0955-9. short: Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019). date_created: 2019-11-12T12:41:44Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-30T07:20:32Z day: '01' ddc: - '510' - '515' - '518' department: - _id: VlKo doi: 10.1007/s40314-019-0955-9 ec_funded: 1 external_id: arxiv: - '2101.09081' isi: - '000488973100005' has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s40314-019-0955-9 month: '12' oa: 1 oa_version: Published Version project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Computational and Applied Mathematics publication_identifier: eissn: - 1807-0302 issn: - 2238-3603 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Convergence analysis of projection method for variational inequalities type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '7001' acknowledged_ssus: - _id: PreCl - _id: Bio article_processing_charge: No article_type: original author: - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 - first_name: Shayan full_name: Shamipour, Shayan id: 40B34FE2-F248-11E8-B48F-1D18A9856A87 last_name: Shamipour - first_name: Kornelija full_name: Pranjic-Ferscha, Kornelija id: 4362B3C2-F248-11E8-B48F-1D18A9856A87 last_name: Pranjic-Ferscha - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: M full_name: Balda, M last_name: Balda - first_name: M full_name: Tada, M last_name: Tada - first_name: K full_name: Matter, K last_name: Matter - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006 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. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006 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.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006. ieee: C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019. 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.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006. 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. date_created: 2019-11-12T12:51:06Z date_published: 2019-10-31T00:00:00Z date_updated: 2024-03-25T23:30:21Z day: '31' ddc: - '570' department: - _id: CaHe - _id: BjHo doi: 10.1016/j.cell.2019.10.006 ec_funded: 1 external_id: isi: - '000493898000012' pmid: - '31675500' file: - access_level: open_access checksum: 33dac4bb77ee630e2666e936b4d57980 content_type: application/pdf creator: dernst date_created: 2020-10-21T07:09:45Z date_updated: 2020-10-21T07:09:45Z file_id: '8684' file_name: 2019_Cell_Schwayer_accepted.pdf file_size: 8805878 relation: main_file success: 1 file_date_updated: 2020-10-21T07:09:45Z has_accepted_license: '1' intvolume: ' 179' isi: 1 issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 937-952.e18 pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News auf IST Website relation: press_release url: https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/ record: - id: '7186' relation: dissertation_contains status: public - id: '8350' relation: dissertation_contains status: public scopus_import: '1' status: public title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 179 year: '2019' ... --- _id: '7002' 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. article_number: '37' article_processing_charge: No article_type: original author: - first_name: Ivo full_name: Kondapaneni, Ivo last_name: Kondapaneni - first_name: Petr full_name: Vevoda, Petr last_name: Vevoda - first_name: Pascal full_name: Grittmann, Pascal last_name: Grittmann - first_name: Tomas full_name: Skrivan, Tomas id: 486A5A46-F248-11E8-B48F-1D18A9856A87 last_name: Skrivan - first_name: Philipp full_name: Slusallek, Philipp last_name: Slusallek - first_name: Jaroslav full_name: Křivánek, Jaroslav last_name: Křivánek citation: ama: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323009 apa: Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., & Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323009 chicago: Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009. ieee: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019. 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.” ACM Transactions on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009. short: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019). date_created: 2019-11-12T13:05:40Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-30T07:21:25Z day: '01' department: - _id: ChWo doi: 10.1145/3306346.3323009 ec_funded: 1 external_id: isi: - '000475740600011' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng month: '07' oa_version: None project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Optimal multiple importance sampling type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '7005' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Michael A. full_name: Cousin, Michael A. last_name: Cousin citation: ama: Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862 apa: Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862 chicago: Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14862. ieee: G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019. 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.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:10.1111/jnc.14862. short: G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583. date_created: 2019-11-12T14:37:08Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-30T07:21:50Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1111/jnc.14862 external_id: isi: - '000490703100001' pmid: - '31479508' file: - access_level: open_access checksum: ec1fb2aebb874009bc309adaada6e1d7 content_type: application/pdf creator: dernst date_created: 2020-02-05T10:30:02Z date_updated: 2020-07-14T12:47:47Z file_id: '7452' file_name: 2019_JournNeurochemistry_Cheung.pdf file_size: 4334962 relation: main_file file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' intvolume: ' 151' isi: 1 issue: '5' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 570-583 pmid: 1 publication: Journal of Neurochemistry publication_identifier: eissn: - 1471-4159 issn: - 0022-3042 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 151 year: '2019' ... --- _id: '7007' abstract: - lang: eng 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.' article_number: '218' article_type: original arxiv: 1 author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: S. Hamed full_name: Hassani, S. Hamed last_name: Hassani - first_name: Rüdiger full_name: Urbanke, Rüdiger last_name: Urbanke citation: ama: Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218 apa: Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218 chicago: Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218. ieee: M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019. ista: Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218. mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218. short: M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019). date_created: 2019-11-12T14:46:19Z date_published: 2019-10-18T00:00:00Z date_updated: 2023-02-23T12:49:28Z day: '18' ddc: - '510' department: - _id: MaMo doi: 10.3390/a12100218 external_id: arxiv: - '1801.03153' file: - access_level: open_access checksum: 267756d8f9db572f496cd1663c89d59a content_type: application/pdf creator: dernst date_created: 2019-11-12T14:48:45Z date_updated: 2020-07-14T12:47:47Z file_id: '7008' file_name: 2019_Algorithms_Mondelli.pdf file_size: 696791 relation: main_file file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' intvolume: ' 12' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Algorithms publication_identifier: issn: - 1999-4893 publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '6675' relation: earlier_version status: public scopus_import: 1 status: public title: A new coding paradigm for the primitive relay channel tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '7009' 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. article_processing_charge: No article_type: review author: - first_name: KM full_name: Yamada, KM last_name: Yamada - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9 apa: Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9 chicago: Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9. ieee: K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019. 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.” Nature Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:10.1038/s41580-019-0172-9. short: K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752. date_created: 2019-11-12T14:54:42Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-30T07:22:20Z day: '01' department: - _id: MiSi doi: 10.1038/s41580-019-0172-9 external_id: isi: - '000497966900007' pmid: - '31582855' intvolume: ' 20' isi: 1 issue: '12' language: - iso: eng month: '12' oa_version: None page: 738–752 pmid: 1 publication: Nature Reviews Molecular Cell Biology publication_identifier: eissn: - 1471-0080 issn: - 1471-0072 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mechanisms of 3D cell migration type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '7010' 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. article_number: 110760V article_processing_charge: No author: - first_name: Heather S. full_name: Davies, Heather S. last_name: Davies - first_name: Natalia S. full_name: Baranova, Natalia S. id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Nouha full_name: El Amri, Nouha last_name: El Amri - first_name: Liliane full_name: Coche-Guérente, Liliane last_name: Coche-Guérente - first_name: Claude full_name: Verdier, Claude last_name: Verdier - first_name: Lionel full_name: Bureau, Lionel last_name: Bureau - first_name: Ralf P. full_name: Richter, Ralf P. last_name: Richter - first_name: Delphine full_name: Débarre, 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: Advances in Microscopic Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058' 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 Advances in Microscopic Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058' 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 Advances in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058. ieee: H. S. Davies et al., “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in Advances in Microscopic Imaging II, Munich, Germany, 2019, vol. 11076. 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. mla: Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” Advances in Microscopic Imaging II, vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058. 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. conference: end_date: 2019-06-27 location: Munich, Germany name: European Conferences on Biomedical Optics start_date: 2019-06-26 date_created: 2019-11-12T15:10:18Z date_published: 2019-07-22T00:00:00Z date_updated: 2023-08-29T06:54:38Z day: '22' department: - _id: MaLo doi: 10.1117/12.2527058 external_id: isi: - '000535353000023' intvolume: ' 11076' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf month: '07' oa: 1 oa_version: Published Version publication: Advances in Microscopic Imaging II publication_identifier: isbn: - '9781510628458' issn: - 1605-7422 publication_status: published publisher: SPIE quality_controlled: '1' scopus_import: '1' status: public title: Blood cell-vessel wall interactions probed by reflection interference contrast microscopy type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11076 year: '2019' ... --- _id: '7013' 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. article_number: '134504' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Tuure full_name: Orell, Tuure last_name: Orell - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Matti full_name: Silveri, Matti last_name: Silveri citation: ama: Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 2019;100(13). doi:10.1103/physrevb.100.134504 apa: Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504 chicago: Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504. ieee: T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” Physical Review B, vol. 100, no. 13. American Physical Society, 2019. 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.” Physical Review B, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:10.1103/physrevb.100.134504. short: T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019). date_created: 2019-11-13T08:25:48Z date_published: 2019-10-01T00:00:00Z date_updated: 2024-02-28T13:13:13Z day: '01' department: - _id: MaSe doi: 10.1103/physrevb.100.134504 external_id: arxiv: - '1907.04043' isi: - '000489036500004' intvolume: ' 100' isi: 1 issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.04043 month: '10' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Probing the many-body localization phase transition with superconducting circuits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2019' ... --- _id: '7014' 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." article_number: '20' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei last_name: Fu - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 citation: ama: Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3339984 apa: Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3339984 chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984. ieee: K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019. 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. mla: Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 20, ACM, 2019, doi:10.1145/3339984. short: K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019). date_created: 2019-11-13T08:33:43Z date_published: 2019-10-01T00:00:00Z date_updated: 2025-06-02T08:53:47Z day: '01' department: - _id: KrCh doi: 10.1145/3339984 ec_funded: 1 external_id: arxiv: - '1705.00317' isi: - '000564108400001' intvolume: ' 41' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.00317 month: '10' oa: 1 oa_version: Preprint project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _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 publication: ACM Transactions on Programming Languages and Systems publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '639' relation: earlier_version status: public - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: Non-polynomial worst-case analysis of recursive programs type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 41 year: '2019' ... --- _id: '7015' abstract: - lang: eng 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. article_number: '035127' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Elliott H. full_name: Lieb, Elliott H. last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127 apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.035127 chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127. ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical Society, 2019. ista: Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127. mla: Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:10.1103/physrevb.100.035127. short: M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019). date_created: 2019-11-13T08:41:48Z date_published: 2019-07-25T00:00:00Z date_updated: 2024-02-28T13:13:23Z day: '25' department: - _id: RoSe doi: 10.1103/physrevb.100.035127 ec_funded: 1 external_id: arxiv: - '1905.09138' isi: - '000477888200001' intvolume: ' 100' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.09138 month: '07' oa: 1 oa_version: Preprint project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Floating Wigner crystal with no boundary charge fluctuations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2019' ... --- _id: '7016' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Isabella full_name: Tomanek, Isabella id: 3981F020-F248-11E8-B48F-1D18A9856A87 last_name: Tomanek orcid: 0000-0001-6197-363X citation: ama: Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016 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. https://doi.org/10.15479/AT:ISTA:7016 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. https://doi.org/10.15479/AT:ISTA:7016. 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. 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, 10.15479/AT:ISTA:7016. mla: Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016. short: I. Tomanek, (2019). contributor: - contributor_type: project_leader first_name: Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 date_created: 2019-11-13T09:07:31Z date_published: 2019-11-13T00:00:00Z date_updated: 2024-02-21T12:45:25Z day: '13' ddc: - '576' department: - _id: CaGu doi: 10.15479/AT:ISTA:7016 file: - access_level: open_access checksum: 72441055043eda4cbf1398a422e2c118 content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:52:21Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 1 - amplified. file_id: '7017' file_name: D8_S35_R2_001.fastq file_size: 2456192500 relation: main_file title: Locus1_amplified - access_level: open_access checksum: a4ac50bf655d9c751f0305ade5c2ee16 content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:52:59Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 1 - ancestral. file_id: '7018' file_name: IT028_S11_R2_001.fastq file_size: 2833452234 relation: main_file title: Locus1_ancestral - access_level: open_access checksum: 5b227708ff478ca06e3f0448a4efdc2f content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:54:10Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 1 - amplified, after DOG-selection. file_id: '7019' file_name: D8-DOG1_S47_R2_001.fastq file_size: 2878017264 relation: main_file title: Locus1_amplified_DOG - access_level: open_access checksum: d9550a4c044116075fa83f8f2ea31d6f content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:54:27Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 2 - amplified. file_id: '7020' file_name: D4_S71_R2_001.fastq file_size: 2180826995 relation: main_file title: Locus2_amplified - access_level: open_access checksum: 466ceb302c020ac013007a879fcde69d content_type: application/octet-stream creator: itomanek date_created: 2019-11-13T08:55:58Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 2 - ancestral. file_id: '7021' file_name: IT030_S23_R2_001.fastq file_size: 2108826444 relation: main_file title: Locus2_ancestral - access_level: open_access checksum: 8aeb1da771713c7baa5a847eff889604 content_type: application/octet-stream creator: itomanek date_created: 2019-11-21T12:31:01Z date_updated: 2020-07-14T12:47:47Z description: Illumina whole genome sequence data for Locus 2 - amplified, after DOG-selection. file_id: '7092' file_name: D4-DOG1_S83_R2_001.fastq file_size: 3144330494 relation: main_file title: Locus2_amplified_DOG - access_level: open_access checksum: bf7d4b053f14af4655fb5574209fdb2d content_type: application/zip creator: itomanek date_created: 2020-01-14T11:22:27Z date_updated: 2020-07-14T12:47:47Z description: Compressed genbank file format containing the sequence of the chromosomal reporter gene cassette. file_id: '7273' file_name: galK_dual_reporter_cassette.gb.zip file_size: 4179 relation: main_file title: DNA sequence of the chromosomal reporter gene cassette - access_level: open_access checksum: 5e91cee2eff6f4a7cde456c6fb07c2ff content_type: text/plain creator: dernst date_created: 2020-01-15T14:15:55Z date_updated: 2020-07-14T12:47:47Z file_id: '7335' file_name: Readme_7016.txt file_size: 435 relation: main_file title: Read_me_sequence_data - access_level: open_access checksum: 5e6745dcfb9c1b11dd935ac3ee45fe33 content_type: application/zip creator: itomanek date_created: 2020-01-22T15:44:16Z date_updated: 2020-07-14T12:47:47Z description: FACS data associated with Fig. 2c - see read_me_FACS file_id: '7351' file_name: FACS_data.xlsx.zip file_size: 3765861 relation: main_file title: FACS data - access_level: open_access checksum: a85caf092ae4b17668f70af2d93fad00 content_type: text/rtf creator: itomanek date_created: 2020-01-22T15:44:16Z date_updated: 2020-07-14T12:47:47Z file_id: '7352' file_name: read_me_FACS.rtf file_size: 4996 relation: main_file - access_level: open_access checksum: fd8ba5d75d24e47ddf7e70bfdadb40d4 content_type: text/rtf creator: itomanek date_created: 2020-01-22T15:44:16Z date_updated: 2020-07-14T12:47:47Z file_id: '7353' file_name: read_me_microfluidics.rtf file_size: 868 relation: main_file - access_level: open_access checksum: 69c5dc5ca5c069a138183c934acc1778 content_type: application/zip creator: itomanek date_created: 2020-01-22T15:44:17Z date_updated: 2020-07-14T12:47:47Z description: microfluidics time trace data - see read_me_microfluidics file_id: '7354' file_name: microfuidics_data.zip file_size: 8141727 relation: main_file title: microfluidics data file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' keyword: - Escherichia coli - gene amplification - galactose - DOG - experimental evolution - Illumina sequence data - FACS data - microfluidics data month: '11' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '7652' relation: used_in_publication status: public status: public title: Data for the paper "Gene amplification as a form of population-level gene expression regulation" type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7026' abstract: - lang: eng 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. acknowledged_ssus: - _id: LifeSc article_processing_charge: No article_type: original author: - first_name: Martin full_name: Lukacisin, Martin id: 298FFE8C-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisin orcid: 0000-0001-6549-4177 - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3. doi:10.1016/j.cels.2019.10.004 apa: Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2019.10.004 chicago: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004. ieee: M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” Cell Systems, vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019. 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. mla: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004. short: M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3. date_created: 2019-11-15T10:51:42Z date_published: 2019-11-27T00:00:00Z date_updated: 2023-08-30T07:24:58Z day: '27' ddc: - '570' department: - _id: ToBo doi: 10.1016/j.cels.2019.10.004 external_id: isi: - '000499495400003' file: - access_level: open_access checksum: 7a11d6c2f9523d65b049512d61733178 content_type: application/pdf creator: dernst date_created: 2019-11-15T10:57:42Z date_updated: 2020-07-14T12:47:48Z file_id: '7027' file_name: 2019_CellSystems_Lukacisin.pdf file_size: 4238460 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '5' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 423-433.e1-e3 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Cell Systems publication_identifier: issn: - 2405-4712 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Emergent gene expression responses to drug combinations predict higher-order drug interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ...