--- _id: '5817' abstract: - lang: eng text: We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion. article_processing_charge: No article_type: original author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: A. full_name: Sakashita, A. last_name: Sakashita - first_name: H. full_name: Noguchi, H. last_name: Noguchi - first_name: P. full_name: Ziherl, P. last_name: Ziherl citation: ama: Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h apa: Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h chicago: Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h. ieee: B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019. ista: Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614. mla: Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h. short: B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614. date_created: 2019-01-11T07:37:47Z date_published: 2019-01-10T00:00:00Z date_updated: 2023-09-13T08:47:16Z day: '10' ddc: - '530' department: - _id: GaTk doi: 10.1039/c8sm01956h external_id: isi: - '000457329700003' pmid: - '30629082' file: - access_level: open_access checksum: 614c337d6424ccd3d48d1b1f9513510d content_type: application/pdf creator: bkavcic date_created: 2020-10-09T11:00:05Z date_updated: 2020-10-09T11:00:05Z file_id: '8641' file_name: lmt_sftmtr_V8.pdf file_size: 5370762 relation: main_file success: 1 file_date_updated: 2020-10-09T11:00:05Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '4' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 602-614 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Limiting shapes of confined lipid vesicles tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 15 year: '2019' ... --- _id: '73' abstract: - lang: eng text: We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest. article_number: '19' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Matthias full_name: Erbar, Matthias last_name: Erbar - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Melchior full_name: Wirth, Melchior last_name: Wirth citation: ama: Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1 apa: Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1 chicago: Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1. ieee: M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019. ista: Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19. mla: Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1. short: M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019). date_created: 2018-12-11T11:44:29Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-09-13T09:12:35Z day: '01' ddc: - '510' department: - _id: JaMa doi: 10.1007/s00526-018-1456-1 ec_funded: 1 external_id: arxiv: - '1805.06040' isi: - '000452849400001' file: - access_level: open_access checksum: ba05ac2d69de4c58d2cd338b63512798 content_type: application/pdf creator: dernst date_created: 2019-01-28T15:37:11Z date_updated: 2020-07-14T12:47:55Z file_id: '5895' file_name: 2018_Calculus_Erbar.pdf file_size: 645565 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 58' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: ' F06504' name: Taming Complexity in Partial Di erential Systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Calculus of Variations and Partial Differential Equations publication_identifier: issn: - '09442669' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: On the geometry of geodesics in discrete optimal transport 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 58 year: '2019' ... --- _id: '14190' abstract: - lang: eng text: "Learning meaningful and compact representations with disentangled semantic\r\naspects is considered to be of key importance in representation learning. Since\r\nreal-world data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose a novel data-set which consists of over one million images of\r\nphysical 3D objects with seven factors of variation, such as object color,\r\nshape, size and position. In order to be able to control all the factors of\r\nvariation precisely, we built an experimental platform where the objects are\r\nbeing moved by a robotic arm. In addition, we provide two more datasets which\r\nconsist of simulations of the experimental setup. These datasets provide for\r\nthe first time the possibility to systematically investigate how well different\r\ndisentanglement methods perform on real data in comparison to simulation, and\r\nhow simulated data can be leveraged to build better representations of the real\r\nworld. We provide a first experimental study of these questions and our results\r\nindicate that learned models transfer poorly, but that model and hyperparameter\r\nselection is an effective means of transferring information to the real world." article_processing_charge: No author: - first_name: Muhammad Waleed full_name: Gondal, Muhammad Waleed last_name: Gondal - first_name: Manuel full_name: Wüthrich, Manuel last_name: Wüthrich - first_name: Đorđe full_name: Miladinović, Đorđe last_name: Miladinović - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Martin full_name: Breidt, Martin last_name: Breidt - first_name: Valentin full_name: Volchkov, Valentin last_name: Volchkov - first_name: Joel full_name: Akpo, Joel last_name: Akpo - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer citation: ama: 'Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.' apa: 'Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.' chicago: 'Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information Processing Systems, Vol. 32, 2019.' ieee: 'M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.' ista: 'Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.' mla: 'Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, vol. 32, 2019.' short: M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019. conference: end_date: 2019-12-14 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2019-12-08 date_created: 2023-08-22T14:09:13Z date_published: 2019-06-07T00:00:00Z date_updated: 2023-09-13T09:46:38Z day: '07' department: - _id: FrLo extern: '1' external_id: arxiv: - '1906.03292' intvolume: ' 32' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.03292 month: '06' oa: 1 oa_version: Preprint publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713807933' publication_status: published quality_controlled: '1' status: public title: 'On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2019' ... --- _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 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: '6894' abstract: - lang: eng text: "Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 citation: ama: Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894 apa: Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894 chicago: Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894. ieee: M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019. ista: Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria. mla: Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894. short: M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019. date_created: 2019-09-22T14:08:44Z date_published: 2019-09-30T00:00:00Z date_updated: 2023-09-19T09:30:43Z day: '30' ddc: - '000' degree_awarded: PhD department: - _id: ToHe doi: 10.15479/AT:ISTA:6894 file: - access_level: open_access checksum: 773beaf4a85dc2acc2c12b578fbe1965 content_type: application/pdf creator: mgiacobbe date_created: 2019-09-27T14:15:05Z date_updated: 2020-07-14T12:47:43Z file_id: '6916' file_name: giacobbe_thesis.pdf file_size: 4100685 relation: main_file - access_level: closed checksum: 97f1c3da71feefd27e6e625d32b4c75b content_type: application/gzip creator: mgiacobbe date_created: 2019-09-27T14:22:04Z date_updated: 2020-07-14T12:47:43Z file_id: '6917' file_name: giacobbe_thesis_src.tar.gz file_size: 7959732 relation: source_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '132' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '631' relation: part_of_dissertation status: public - id: '647' relation: part_of_dissertation status: public - id: '140' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 title: Automatic time-unbounded reachability analysis of hybrid systems 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '9805' abstract: - lang: eng text: The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event? article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4' apa: 'Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4' chicago: 'Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.' ieee: 'N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.' ista: 'Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.' mla: 'Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.' short: N.H. Barton, (2019). date_created: 2021-08-06T12:03:50Z date_published: 2019-01-09T00:00:00Z date_updated: 2023-09-19T10:06:07Z day: '09' department: - _id: NiBa doi: 10.5061/dryad.2kb6fh4 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.2kb6fh4 month: '01' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '40' relation: used_in_publication status: public status: public title: 'Data from: The consequences of an introgression event' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '8' abstract: - lang: eng text: Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification. acknowledgement: This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Trébuchet, Guillaume last_name: Trébuchet - first_name: Pierre B full_name: Cattenoz, Pierre B last_name: Cattenoz - first_name: János full_name: Zsámboki, János last_name: Zsámboki - first_name: David full_name: Mazaud, David last_name: Mazaud - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Manolis full_name: Fanto, Manolis last_name: Fanto - first_name: Angela full_name: Giangrande, Angela last_name: Giangrande citation: ama: Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 2019;39(2):238-255. doi:10.1523/JNEUROSCI.1059-18.2018 apa: Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., & Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1059-18.2018 chicago: Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience. Society for Neuroscience, 2019. https://doi.org/10.1523/JNEUROSCI.1059-18.2018. ieee: G. Trébuchet et al., “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” Journal of Neuroscience, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019. ista: Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255. mla: Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:10.1523/JNEUROSCI.1059-18.2018. short: G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255. date_created: 2018-12-11T11:44:07Z date_published: 2019-01-09T00:00:00Z date_updated: 2023-09-19T10:10:55Z day: '09' ddc: - '570' department: - _id: DaSi doi: 10.1523/JNEUROSCI.1059-18.2018 ec_funded: 1 external_id: isi: - '000455189900006' pmid: - '30504274' file: - access_level: open_access checksum: 8f6925eb4cd1e8747d8ea25929c68de6 content_type: application/pdf creator: dernst date_created: 2020-10-02T09:33:28Z date_updated: 2020-10-02T09:33:28Z file_id: '8596' file_name: 2019_JournNeuroscience_Trebuchet.pdf file_size: 9455414 relation: main_file success: 1 file_date_updated: 2020-10-02T09:33:28Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 238-255 pmid: 1 project: - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '8048' quality_controlled: '1' scopus_import: '1' status: public title: The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 39 year: '2019' ... --- _id: '5' abstract: - lang: eng text: In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2. article_processing_charge: Yes (via OA deal) author: - first_name: Iordan V full_name: Ganev, Iordan V id: 447491B8-F248-11E8-B48F-1D18A9856A87 last_name: Ganev citation: ama: Ganev IV. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 2019;99(3):778-806. doi:10.1112/jlms.12193 apa: Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193 chicago: Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12193. ieee: I. V. Ganev, “The wonderful compactification for quantum groups,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019. ista: Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806. mla: Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:10.1112/jlms.12193. short: I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806. date_created: 2018-12-11T11:44:06Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-19T10:13:08Z day: '01' ddc: - '510' department: - _id: TaHa doi: 10.1112/jlms.12193 external_id: isi: - '000470025900008' file: - access_level: open_access checksum: 1be56239b2cd740a0e9a084f773c22f6 content_type: application/pdf creator: kschuh date_created: 2020-01-07T13:31:53Z date_updated: 2020-07-14T12:46:35Z file_id: '7238' file_name: 2019_Wiley_Ganev.pdf file_size: 431754 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 99' isi: 1 issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 778-806 publication: Journal of the London Mathematical Society publication_status: published publisher: Wiley publist_id: '8052' quality_controlled: '1' scopus_import: '1' status: public title: The wonderful compactification for quantum groups 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 99 year: '2019' ... --- _id: '7172' abstract: - lang: eng text: "The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes." acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mina K full_name: Vasileva, Mina K id: 3407EB18-F248-11E8-B48F-1D18A9856A87 last_name: Vasileva citation: ama: Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:10.15479/AT:ISTA:7172 apa: Vasileva, M. K. (2019). Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7172 chicago: Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7172. ieee: M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019. ista: Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria. mla: Vasileva, Mina K. Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7172. short: M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019. date_created: 2019-12-11T21:24:39Z date_published: 2019-12-12T00:00:00Z date_updated: 2023-09-19T10:39:33Z day: '12' ddc: - '570' degree_awarded: PhD department: - _id: JiFr doi: 10.15479/AT:ISTA:7172 file: - access_level: closed checksum: ef981c1a3b1d9da0edcbedcff4970d37 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mvasilev date_created: 2019-12-12T09:32:36Z date_updated: 2020-07-14T12:47:51Z file_id: '7175' file_name: Thesis_Mina_final_upload_7.docx file_size: 20454014 relation: source_file - access_level: open_access checksum: 3882c4585e46c9cfb486e4225cad54ab content_type: application/pdf creator: mvasilev date_created: 2019-12-12T09:33:10Z date_updated: 2020-07-14T12:47:51Z file_id: '7176' file_name: Thesis_Mina_final_upload_7.pdf file_size: 11565025 relation: main_file file_date_updated: 2020-07-14T12:47:51Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '192' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1346' relation: part_of_dissertation status: public - id: '6377' relation: part_of_dissertation status: public - id: '449' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '6093' abstract: - lang: eng text: Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source. article_number: e0212699 article_processing_charge: No author: - first_name: Mohammad full_name: Goudarzi, Mohammad id: 3384113A-F248-11E8-B48F-1D18A9856A87 last_name: Goudarzi - first_name: Aleix full_name: Boquet-Pujadas, Aleix last_name: Boquet-Pujadas - first_name: Jean Christophe full_name: Olivo-Marin, Jean Christophe last_name: Olivo-Marin - first_name: Erez full_name: Raz, Erez last_name: Raz citation: ama: Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 2019;14(2). doi:10.1371/journal.pone.0212699 apa: Goudarzi, M., Boquet-Pujadas, A., Olivo-Marin, J. C., & Raz, E. (2019). Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0212699 chicago: Goudarzi, Mohammad, Aleix Boquet-Pujadas, Jean Christophe Olivo-Marin, and Erez Raz. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0212699. ieee: M. Goudarzi, A. Boquet-Pujadas, J. C. Olivo-Marin, and E. Raz, “Fluid dynamics during bleb formation in migrating cells in vivo,” PLOS ONE, vol. 14, no. 2. Public Library of Science, 2019. ista: Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. 2019. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 14(2), e0212699. mla: Goudarzi, Mohammad, et al. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE, vol. 14, no. 2, e0212699, Public Library of Science, 2019, doi:10.1371/journal.pone.0212699. short: M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019). date_created: 2019-03-10T22:59:21Z date_published: 2019-02-26T00:00:00Z date_updated: 2023-09-19T14:46:47Z day: '26' ddc: - '570' department: - _id: Bio doi: 10.1371/journal.pone.0212699 external_id: isi: - '000459712100022' file: - access_level: open_access checksum: b885de050ed4bb3c86f706487a47197f content_type: application/pdf creator: dernst date_created: 2019-03-11T16:09:23Z date_updated: 2020-07-14T12:47:19Z file_id: '6096' file_name: 2019_PLoSOne_Goudarzi.pdf file_size: 2967731 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: PLOS ONE publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Fluid dynamics during bleb formation in migrating cells in vivo 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2019' ... --- _id: '6473' abstract: - lang: eng text: "Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sarah A full_name: Cepeda Humerez, Sarah A id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87 last_name: Cepeda Humerez citation: ama: Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473 apa: Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473 chicago: Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473. ieee: S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019. ista: Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria. mla: Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473. short: S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019. date_created: 2019-05-21T00:11:23Z date_published: 2019-05-23T00:00:00Z date_updated: 2023-09-19T15:13:26Z day: '23' ddc: - '004' degree_awarded: PhD department: - _id: GaTk doi: 10.15479/AT:ISTA:6473 file: - access_level: closed checksum: 75f9184c1346e10a5de5f9cc7338309a content_type: application/zip creator: scepeda date_created: 2019-05-23T11:18:16Z date_updated: 2020-07-14T12:47:31Z file_id: '6480' file_name: Thesis_Cepeda.zip file_size: 23937464 relation: source_file - access_level: open_access checksum: afdc0633ddbd71d5b13550d7fb4f4454 content_type: application/pdf creator: scepeda date_created: 2019-05-23T11:18:13Z date_updated: 2020-07-14T12:47:31Z file_id: '6481' file_name: CepedaThesis.pdf file_size: 16646985 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' keyword: - Information estimation - Time-series - data analysis language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '135' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1576' relation: dissertation_contains status: public - id: '6900' relation: dissertation_contains status: public - id: '281' relation: dissertation_contains status: public - id: '2016' relation: dissertation_contains status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Estimating information flow in single 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '6071' abstract: - lang: eng text: 'Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak citation: ama: Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071 apa: Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071 chicago: Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071. ieee: R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019. ista: Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. mla: Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071. short: R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019. date_created: 2019-03-06T16:16:10Z date_published: 2019-03-11T00:00:00Z date_updated: 2023-09-22T10:00:48Z day: '11' ddc: - '576' degree_awarded: PhD department: - _id: GaTk - _id: NiBa doi: 10.15479/at:ista:th6071 file: - access_level: open_access checksum: e60a72de35d270b31f1a23d50f224ec0 content_type: application/pdf creator: rprizak date_created: 2019-03-06T16:05:07Z date_updated: 2020-07-14T12:47:18Z file_id: '6072' file_name: Thesis_final_PDFA_RoshanPrizak.pdf file_size: 20995465 relation: main_file - access_level: closed checksum: 67c2630333d05ebafef5f018863a8465 content_type: application/zip creator: rprizak date_created: 2019-03-06T16:09:39Z date_updated: 2020-07-14T12:47:18Z file_id: '6073' file_name: thesis_v2_merge.zip file_size: 85705272 relation: source_file title: Latex files file_date_updated: 2020-07-14T12:47:18Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '189' project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1358' relation: part_of_dissertation status: public - id: '955' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Coevolution of transcription factors and their binding sites in sequence space type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '7436' abstract: - lang: eng text: 'For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. ' article_processing_charge: No article_type: original author: - first_name: Tanya K full_name: Srivastava, Tanya K id: 4D046628-F248-11E8-B48F-1D18A9856A87 last_name: Srivastava citation: ama: Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177 apa: Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177 chicago: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177. ieee: T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019. ista: Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177. mla: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177. short: T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177. date_created: 2020-02-02T23:01:06Z date_published: 2019-05-20T00:00:00Z date_updated: 2023-10-17T07:42:21Z day: '20' ddc: - '510' department: - _id: TaHa doi: 10.25537/dm.2019v24.1135-1177 external_id: arxiv: - '1809.08970' isi: - '000517806400019' file: - access_level: open_access checksum: 9a1a64bd49ab03fa4f738fb250fc4f90 content_type: application/pdf creator: dernst date_created: 2020-02-03T06:26:12Z date_updated: 2020-07-14T12:47:58Z file_id: '7438' file_name: 2019_DocumMath_Srivastava.pdf file_size: 469730 relation: main_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' intvolume: ' 24' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1135-1177 publication: Documenta Mathematica publication_identifier: eissn: - 1431-0643 issn: - 1431-0635 publication_status: published publisher: EMS Press quality_controlled: '1' scopus_import: '1' status: public title: On derived equivalences of k3 surfaces in positive characteristic 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: 24 year: '2019' ... --- _id: '72' abstract: - lang: eng text: We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t. article_processing_charge: No article_type: original author: - first_name: Patrick full_name: Ferrari, Patrick last_name: Ferrari - first_name: Promit full_name: Ghosal, Promit last_name: Ghosal - first_name: Peter full_name: Nejjar, Peter id: 4BF426E2-F248-11E8-B48F-1D18A9856A87 last_name: Nejjar citation: ama: Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916 apa: Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916 chicago: Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AIHP916. ieee: P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019. ista: Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225. mla: Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:10.1214/18-AIHP916. short: P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225. date_created: 2018-12-11T11:44:29Z date_published: 2019-09-25T00:00:00Z date_updated: 2023-10-17T08:53:45Z day: '25' department: - _id: LaEr - _id: JaMa doi: 10.1214/18-AIHP916 ec_funded: 1 external_id: arxiv: - '1710.02323' isi: - '000487763200001' intvolume: ' 55' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1710.02323 month: '09' oa: 1 oa_version: Preprint page: 1203-1225 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication: Annales de l'institut Henri Poincare (B) Probability and Statistics publication_identifier: issn: - 0246-0203 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Limit law of a second class particle in TASEP with non-random initial condition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2019' ... --- _id: '6657' abstract: - lang: eng text: 'In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as "gold" and "green" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.' article_processing_charge: No article_type: original author: - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 citation: ama: Danowski P. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2019;72(1):59-65. doi:10.31263/voebm.v72i1.2276 apa: Danowski, P. (2019). An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v72i1.2276 chicago: Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. https://doi.org/10.31263/voebm.v72i1.2276. ieee: P. Danowski, “An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 59–65, 2019. ista: Danowski P. 2019. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65. mla: Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019, pp. 59–65, doi:10.31263/voebm.v72i1.2276. short: P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 72 (2019) 59–65. date_created: 2019-07-21T21:59:15Z date_published: 2019-05-17T00:00:00Z date_updated: 2023-10-17T11:33:58Z day: '17' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v72i1.2276 file: - access_level: open_access checksum: c0d2695d6d0d34e62ba06fb3f0ebaaed content_type: application/pdf creator: apreinsp date_created: 2019-07-22T08:45:03Z date_updated: 2020-07-14T12:47:35Z file_id: '6661' file_name: 2019_MitteilungenDerVOEB_Danowski.pdf file_size: 468558 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 72' issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 59-65 publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare publication_identifier: eissn: - 1022-2588 publication_status: published publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare quality_controlled: '1' related_material: record: - id: '5686' relation: earlier_version status: public scopus_import: '1' status: public title: An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors 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: 72 year: '2019' ... --- _id: '6646' abstract: - lang: eng text: We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature. article_number: paper JTu2A.52 article_processing_charge: No author: - first_name: Mandeep full_name: Khatoniar, Mandeep last_name: Khatoniar - first_name: Nicholas full_name: Yama, Nicholas last_name: Yama - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Sriram full_name: Guddala, Sriram last_name: Guddala - first_name: Pouyan full_name: Ghaemi, Pouyan last_name: Ghaemi - first_name: Vinod full_name: Menon, Vinod last_name: Menon citation: ama: 'Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications and Technology. Optica  Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52' apa: 'Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., & Menon, V. (2019). Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In CLEO: Applications and Technology. San Jose, CA, United States: Optica  Publishing Group. https://doi.org/10.1364/cleo_at.2019.jtu2a.52' chicago: 'Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, and Vinod Menon. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” In CLEO: Applications and Technology. Optica  Publishing Group, 2019. https://doi.org/10.1364/cleo_at.2019.jtu2a.52.' ieee: 'M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, and V. Menon, “Room temperature control of valley coherence in bilayer WS2 exciton polaritons,” in CLEO: Applications and Technology, San Jose, CA, United States, 2019.' ista: 'Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. 2019. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. CLEO: Applications and Technology. CLEO: Conference on Lasers and Electro-Optics, paper JTu2A.52.' mla: 'Khatoniar, Mandeep, et al. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” CLEO: Applications and Technology, paper JTu2A.52, Optica  Publishing Group, 2019, doi:10.1364/cleo_at.2019.jtu2a.52.' short: 'M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:, CLEO: Applications and Technology, Optica  Publishing Group, 2019.' conference: end_date: 2019-05-10 location: San Jose, CA, United States name: 'CLEO: Conference on Lasers and Electro-Optics' start_date: 2019-05-05 date_created: 2019-07-17T09:40:44Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-10-17T12:14:29Z day: '01' department: - _id: MiLe doi: 10.1364/cleo_at.2019.jtu2a.52 language: - iso: eng month: '05' oa_version: None publication: 'CLEO: Applications and Technology' publication_identifier: isbn: - '9781943580576' publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Room temperature control of valley coherence in bilayer WS2 exciton polaritons type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7233' abstract: - lang: eng text: We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm. article_number: NM2A.5 article_processing_charge: No author: - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: Florian full_name: Sedlmeir, Florian last_name: Sedlmeir - first_name: Gerd full_name: Leuchs, Gerd last_name: Leuchs - first_name: Madhuri full_name: Kumari, Madhuri last_name: Kumari - first_name: Harald G.L. full_name: Schwefel, Harald G.L. last_name: Schwefel citation: ama: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica  Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5' apa: 'Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica  Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5' chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics, OSA Technical Digest. Optica  Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5. ieee: A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019. ista: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.' mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica  Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5. short: A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica  Publishing Group, 2019. conference: end_date: 2019-07-19 location: Waikoloa Beach, Hawaii (HI), United States name: 'NLO: Nonlinear Optics' start_date: 2019-07-15 date_created: 2020-01-05T23:00:48Z date_published: 2019-07-15T00:00:00Z date_updated: 2023-10-17T12:14:46Z day: '15' department: - _id: JoFi doi: 10.1364/NLO.2019.NM2A.5 language: - iso: eng month: '07' oa_version: None publication: Nonlinear Optics, OSA Technical Digest publication_identifier: isbn: - '9781557528209' publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6240' abstract: - lang: eng text: For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles. article_processing_charge: No author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: Yuriy full_name: Nemish, Yuriy id: 4D902E6A-F248-11E8-B48F-1D18A9856A87 last_name: Nemish orcid: 0000-0002-7327-856X citation: ama: Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 2019;55(2):661-696. doi:10.1214/18-AIHP894 apa: Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894 chicago: Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894. ieee: J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of Kronecker random matrices,” Annales de l’institut Henri Poincare, vol. 55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019. ista: Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696. mla: Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:10.1214/18-AIHP894. short: J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696. date_created: 2019-04-08T14:05:04Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-10-17T12:20:20Z day: '01' department: - _id: LaEr doi: 10.1214/18-AIHP894 ec_funded: 1 external_id: arxiv: - '1706.08343' isi: - '000467793600003' intvolume: ' 55' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.08343 month: '05' oa: 1 oa_version: Preprint page: 661-696 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Annales de l'institut Henri Poincare publication_identifier: issn: - 0246-0203 publication_status: published publisher: Institut Henri Poincaré quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: '1' status: public title: Location of the spectrum of Kronecker random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2019' ... --- _id: '7399' abstract: - lang: eng text: Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established. article_number: e1008268 article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Andergassen, Daniel last_name: Andergassen - first_name: Markus full_name: Muckenhuber, Markus last_name: Muckenhuber - first_name: Philipp C. full_name: Bammer, Philipp C. last_name: Bammer - first_name: Tomasz M. full_name: Kulinski, Tomasz M. last_name: Kulinski - first_name: Hans-Christian full_name: Theussl, Hans-Christian last_name: Theussl - first_name: Takahiko full_name: Shimizu, Takahiko last_name: Shimizu - first_name: Josef M. full_name: Penninger, Josef M. last_name: Penninger - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Quanah J. full_name: Hudson, Quanah J. last_name: Hudson citation: ama: Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 2019;15(7). doi:10.1371/journal.pgen.1008268 apa: Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268 chicago: Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler, and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008268. ieee: D. Andergassen et al., “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” PLoS Genetics, vol. 15, no. 7. Public Library of Science, 2019. ista: Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 15(7), e1008268. mla: Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics, vol. 15, no. 7, e1008268, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008268. short: D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl, T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019). date_created: 2020-01-29T16:14:07Z date_published: 2019-07-22T00:00:00Z date_updated: 2023-10-17T12:30:27Z day: '22' ddc: - '570' department: - _id: SiHi doi: 10.1371/journal.pgen.1008268 external_id: isi: - '000478689100025' pmid: - '31329595' file: - access_level: open_access checksum: 2f51fc91e4a4199827adc51d432ad864 content_type: application/pdf creator: dernst date_created: 2020-02-04T10:11:55Z date_updated: 2020-07-14T12:47:57Z file_id: '7446' file_name: 2019_PlosGenetics_Andergassen.pdf file_size: 2302307 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes 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: 15 year: '2019' ... --- _id: '7103' abstract: - lang: eng text: Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics. article_number: e1007268 article_processing_charge: No article_type: original author: - first_name: Jilin W. J. L. full_name: Wang, Jilin W. J. L. last_name: Wang - first_name: Fabrizio full_name: Lombardi, Fabrizio id: A057D288-3E88-11E9-986D-0CF4E5697425 last_name: Lombardi orcid: 0000-0003-2623-5249 - first_name: Xiyun full_name: Zhang, Xiyun last_name: Zhang - first_name: Christelle full_name: Anaclet, Christelle last_name: Anaclet - first_name: Plamen Ch. full_name: Ivanov, Plamen Ch. last_name: Ivanov citation: ama: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268 apa: Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268 chicago: Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268. ieee: J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019. ista: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268. mla: Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007268. short: J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019). date_created: 2019-11-25T08:20:47Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-10-17T12:30:07Z day: '01' ddc: - '570' - '000' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007268 ec_funded: 1 external_id: isi: - '000500976100014' pmid: - '31725712' file: - access_level: open_access checksum: 2a096a9c6dcc6eaa94077b2603bc6c12 content_type: application/pdf creator: dernst date_created: 2019-11-25T08:24:01Z date_updated: 2020-07-14T12:47:49Z file_id: '7104' file_name: 2019_PLOSComBio_Wang.pdf file_size: 3982516 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: PLoS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture 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: 15 year: '2019' ... --- _id: '6569' abstract: - lang: eng text: 'Knowledge distillation, i.e. one classifier being trained on the outputs of another classifier, is an empirically very successful technique for knowledge transfer between classifiers. It has even been observed that classifiers learn much faster and more reliably if trained with the outputs of another classifier as soft labels, instead of from ground truth data. So far, however, there is no satisfactory theoretical explanation of this phenomenon. In this work, we provide the first insights into the working mechanisms of distillation by studying the special case of linear and deep linear classifiers. Specifically, we prove a generalization bound that establishes fast convergence of the expected risk of a distillation-trained linear classifier. From the bound and its proof we extract three keyfactors that determine the success of distillation: data geometry – geometric properties of the datadistribution, in particular class separation, has an immediate influence on the convergence speed of the risk; optimization bias– gradient descentoptimization finds a very favorable minimum of the distillation objective; and strong monotonicity– the expected risk of the student classifier always decreases when the size of the training set grows.' article_processing_charge: No author: - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Phuong M, Lampert C. Towards understanding knowledge distillation. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:5142-5151.' apa: 'Phuong, M., & Lampert, C. (2019). Towards understanding knowledge distillation. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 5142–5151). Long Beach, CA, United States: ML Research Press.' chicago: Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” In Proceedings of the 36th International Conference on Machine Learning, 97:5142–51. ML Research Press, 2019. ieee: M. Phuong and C. Lampert, “Towards understanding knowledge distillation,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 5142–5151. ista: 'Phuong M, Lampert C. 2019. Towards understanding knowledge distillation. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 5142–5151.' mla: Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 5142–51. short: M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 5142–5151. conference: end_date: 2019-06-15 location: Long Beach, CA, United States name: 'ICML: International Conference on Machine Learning' start_date: 2019-06-10 date_created: 2019-06-20T18:23:03Z date_published: 2019-06-13T00:00:00Z date_updated: 2023-10-17T12:31:38Z day: '13' ddc: - '000' department: - _id: ChLa file: - access_level: open_access checksum: a66d00e2694d749250f8507f301320ca content_type: application/pdf creator: bphuong date_created: 2019-06-20T18:22:56Z date_updated: 2020-07-14T12:47:33Z file_id: '6570' file_name: paper.pdf file_size: 686432 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 97' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 5142-5151 publication: Proceedings of the 36th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Towards understanding knowledge distillation type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2019' ... --- _id: '6590' abstract: - lang: eng text: 'Modern machine learning methods often require more data for training than a single expert can provide. Therefore, it has become a standard procedure to collect data from external sources, e.g. via crowdsourcing. Unfortunately, the quality of these sources is not always guaranteed. As additional complications, the data might be stored in a distributed way, or might even have to remain private. In this work, we address the question of how to learn robustly in such scenarios. Studying the problem through the lens of statistical learning theory, we derive a procedure that allows for learning from all available sources, yet automatically suppresses irrelevant or corrupted data. We show by extensive experiments that our method provides significant improvements over alternative approaches from robust statistics and distributed optimization. ' article_processing_charge: No author: - first_name: Nikola H full_name: Konstantinov, Nikola H id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87 last_name: Konstantinov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:3488-3498.' apa: 'Konstantinov, N. H., & Lampert, C. (2019). Robust learning from untrusted sources. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 3488–3498). Long Beach, CA, USA: ML Research Press.' chicago: Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted Sources.” In Proceedings of the 36th International Conference on Machine Learning, 97:3488–98. ML Research Press, 2019. ieee: N. H. Konstantinov and C. Lampert, “Robust learning from untrusted sources,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, USA, 2019, vol. 97, pp. 3488–3498. ista: 'Konstantinov NH, Lampert C. 2019. Robust learning from untrusted sources. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 3488–3498.' mla: Konstantinov, Nikola H., and Christoph Lampert. “Robust Learning from Untrusted Sources.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 3488–98. short: N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498. conference: end_date: 2919-06-15 location: Long Beach, CA, USA name: 'ICML: International Conference on Machine Learning' start_date: 2019-06-10 date_created: 2019-06-27T14:18:23Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-10-17T12:31:55Z day: '01' department: - _id: ChLa ec_funded: 1 external_id: arxiv: - '1901.10310' intvolume: ' 97' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1901.10310 month: '06' oa: 1 oa_version: Preprint page: 3488-3498 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Proceedings of the 36th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '10799' relation: dissertation_contains status: public scopus_import: '1' status: public title: Robust learning from untrusted sources type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 97 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: '6621' abstract: - lang: eng text: We read with great interest the recent work in PNAS by Bergero et al. (1) describing differences in male and female recombination patterns on the guppy (Poecilia reticulata) sex chromosome. We fully agree that recombination in males is largely confined to the ends of the sex chromosome. Bergero et al. interpret these results to suggest that our previous findings of population-level variation in the degree of sex chromosome differentiation in this species (2) are incorrect. However, we suggest that their results are entirely consistent with our previous report, and that their interpretation presents a false controversy. article_processing_charge: No article_type: letter_note author: - first_name: Alison E. full_name: Wright, Alison E. last_name: Wright - first_name: Iulia full_name: Darolti, Iulia last_name: Darolti - first_name: Natasha I. full_name: Bloch, Natasha I. last_name: Bloch - first_name: Vicencio full_name: Oostra, Vicencio last_name: Oostra - first_name: Benjamin A. full_name: Sandkam, Benjamin A. last_name: Sandkam - first_name: Séverine D. full_name: Buechel, Séverine D. last_name: Buechel - first_name: Niclas full_name: Kolm, Niclas last_name: Kolm - first_name: Felix full_name: Breden, Felix last_name: Breden - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Judith E. full_name: Mank, Judith E. last_name: Mank citation: ama: Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(26):12607-12608. doi:10.1073/pnas.1905555116 apa: Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel, S. D., … Mank, J. E. (2019). On the power to detect rare recombination events. 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.1905555116 chicago: Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith E. Mank. “On the Power to Detect Rare Recombination Events.” 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.1905555116. ieee: A. E. Wright et al., “On the power to detect rare recombination events,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26. Proceedings of the National Academy of Sciences, pp. 12607–12608, 2019. ista: Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 116(26), 12607–12608. mla: Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26, Proceedings of the National Academy of Sciences, 2019, pp. 12607–08, doi:10.1073/pnas.1905555116. short: A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel, N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 12607–12608. date_created: 2019-07-07T21:59:25Z date_published: 2019-06-25T00:00:00Z date_updated: 2023-10-17T12:44:15Z day: '25' department: - _id: BeVi doi: 10.1073/pnas.1905555116 external_id: isi: - '000472719100010' pmid: - '31213531' intvolume: ' 116' isi: 1 issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1905555116 month: '06' oa: 1 oa_version: Published Version page: 12607-12608 pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: On the power to detect rare recombination events type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 116 year: '2019' ... --- _id: '6856' abstract: - lang: eng text: 'Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.' article_processing_charge: No article_type: original author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Yaniv full_name: Brandvain, Yaniv last_name: Brandvain - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Sarah full_name: Yakimowski, Sarah last_name: Yakimowski - first_name: Tanmay full_name: Dixit, Tanmay last_name: Dixit - first_name: Christian full_name: Lexer, Christian last_name: Lexer - first_name: Eva full_name: Cereghetti, Eva id: 71AA91B4-05ED-11EA-8BEB-F5833E63BD63 last_name: Cereghetti - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 citation: ama: 'Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180' apa: 'Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180' chicago: 'Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.' ieee: 'M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.' ista: 'Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.' mla: 'Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.' short: M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047. date_created: 2019-09-07T14:35:40Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-10-18T08:47:08Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/nph.16180 ec_funded: 1 external_id: pmid: - '31505037' file: - access_level: open_access checksum: 21e4c95599bbcaf7c483b89954658672 content_type: application/pdf creator: dernst date_created: 2019-11-13T08:15:05Z date_updated: 2020-07-14T12:47:42Z file_id: '7011' file_name: 2019_NewPhytologist_Pickup.pdf file_size: 1511958 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 224' issue: '3' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1035-1047 pmid: 1 project: - _id: 25B36484-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '329960' name: Mating system and the evolutionary dynamics of hybrid zones - _id: 2662AADE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02463 name: Sex chromosomes and species barriers publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow' 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: 224 year: '2019' ... --- _id: '14299' abstract: - lang: eng text: DNA origami nano-objects are usually designed around generic single-stranded “scaffolds”. Many properties of the target object are determined by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable production methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence composition on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent cross-linking of DNA origami via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding DNA origami domain separation. article_processing_charge: No article_type: original author: - first_name: Engelhardt full_name: FAS, Engelhardt last_name: FAS - first_name: Florian M full_name: Praetorius, Florian M id: dfec9381-4341-11ee-8fd8-faa02bba7d62 last_name: Praetorius - first_name: CH full_name: Wachauf, CH last_name: Wachauf - first_name: G full_name: Brüggenthies, G last_name: Brüggenthies - first_name: F full_name: Kohler, F last_name: Kohler - first_name: B full_name: Kick, B last_name: Kick - first_name: KL full_name: Kadletz, KL last_name: Kadletz - first_name: PN full_name: Pham, PN last_name: Pham - first_name: KL full_name: Behler, KL last_name: Behler - first_name: T full_name: Gerling, T last_name: Gerling - first_name: H full_name: Dietz, H last_name: Dietz citation: ama: FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 2019;13(5):5015-5027. doi:10.1021/acsnano.9b01025 apa: FAS, E., Praetorius, F. M., Wachauf, C., Brüggenthies, G., Kohler, F., Kick, B., … Dietz, H. (2019). Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. ACS Publications. https://doi.org/10.1021/acsnano.9b01025 chicago: FAS, Engelhardt, Florian M Praetorius, CH Wachauf, G Brüggenthies, F Kohler, B Kick, KL Kadletz, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano. ACS Publications, 2019. https://doi.org/10.1021/acsnano.9b01025. ieee: E. FAS et al., “Custom-size, functional, and durable DNA origami with design-specific scaffolds,” ACS Nano, vol. 13, no. 5. ACS Publications, pp. 5015–5027, 2019. ista: FAS E, Praetorius FM, Wachauf C, Brüggenthies G, Kohler F, Kick B, Kadletz K, Pham P, Behler K, Gerling T, Dietz H. 2019. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 13(5), 5015–5027. mla: FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano, vol. 13, no. 5, ACS Publications, 2019, pp. 5015–27, doi:10.1021/acsnano.9b01025. short: E. FAS, F.M. Praetorius, C. Wachauf, G. Brüggenthies, F. Kohler, B. Kick, K. Kadletz, P. Pham, K. Behler, T. Gerling, H. Dietz, ACS Nano 13 (2019) 5015–5027. date_created: 2023-09-06T12:48:47Z date_published: 2019-04-16T00:00:00Z date_updated: 2023-11-07T12:17:31Z day: '16' doi: 10.1021/acsnano.9b01025 extern: '1' external_id: pmid: - '30990672' intvolume: ' 13' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acsnano.9b01025 month: '04' oa: 1 oa_version: Published Version page: 5015-5027 pmid: 1 publication: ACS Nano publication_identifier: eissn: - 1936-086x issn: - 1936-0851 publication_status: published publisher: ACS Publications quality_controlled: '1' scopus_import: '1' status: public title: Custom-size, functional, and durable DNA origami with design-specific scaffolds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2019' ... --- _id: '6647' abstract: - lang: eng text: The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2. alternative_title: - LIPIcs author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Bernd full_name: Gärtner, Bernd last_name: Gärtner - first_name: Andrey full_name: Kupavskii, Andrey last_name: Kupavskii - first_name: Pavel full_name: Valtr, Pavel last_name: Valtr - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38' apa: 'Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019). The crossing Tverberg theorem. In 35th International Symposium on Computational Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38' chicago: Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38. ieee: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13. ista: 'Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.' mla: Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38. short: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13. conference: end_date: 2019-06-21 location: Portland, OR, United States name: 'SoCG 2019: Symposium on Computational Geometry' start_date: 2019-06-18 date_created: 2019-07-17T10:35:04Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-12-13T12:03:35Z day: '01' ddc: - '000' - '510' department: - _id: UlWa doi: 10.4230/LIPICS.SOCG.2019.38 external_id: arxiv: - '1812.04911' file: - access_level: open_access checksum: d6d017f8b41291b94d102294fa96ae9c content_type: application/pdf creator: dernst date_created: 2019-07-24T06:54:52Z date_updated: 2020-07-14T12:47:35Z file_id: '6667' file_name: 2019_LIPICS_Fulek.pdf file_size: 559837 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 129' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 38:1-38:13 project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: 35th International Symposium on Computational Geometry publication_identifier: isbn: - '9783959771047' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '13974' relation: later_version status: public scopus_import: 1 status: public title: The crossing Tverberg theorem 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2019' ... --- _id: '6676' abstract: - lang: eng text: "It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Faith full_name: Ellen, Faith last_name: Ellen - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili - first_name: Leqi full_name: Zhu, Leqi last_name: Zhu citation: ama: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407' apa: 'Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019). Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316407' chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407. ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 986–996. ista: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996.' mla: Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–96, doi:10.1145/3313276.3316407. short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–996. conference: end_date: 2019-06-26 location: Phoenix, AZ, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2019-06-23 date_created: 2019-07-24T09:13:05Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-12-13T12:28:28Z day: '01' department: - _id: DaAl doi: 10.1145/3313276.3316407 external_id: arxiv: - '1811.01421' isi: - '000523199100089' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.01421 month: '06' oa: 1 oa_version: Preprint page: 986-996 publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing publication_identifier: isbn: - '9781450367059' publication_status: published publisher: ACM Press quality_controlled: '1' related_material: record: - id: '14364' relation: later_version status: public scopus_import: '1' status: public title: Why extension-based proofs fail type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '7950' abstract: - lang: eng text: "The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results:\r\n1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices \ have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved." article_number: '1903.06981' article_processing_charge: No author: - first_name: Ahmad full_name: Biniaz, Ahmad last_name: Biniaz - first_name: Kshitij full_name: Jain, Kshitij last_name: Jain - first_name: Anna full_name: Lubiw, Anna last_name: Lubiw - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Tillmann full_name: Miltzow, Tillmann last_name: Miltzow - first_name: Debajyoti full_name: Mondal, Debajyoti last_name: Mondal - first_name: Anurag Murty full_name: Naredla, Anurag Murty last_name: Naredla - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Alexi full_name: Turcotte, Alexi last_name: Turcotte citation: ama: Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv. apa: Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (n.d.). Token swapping on trees. arXiv. chicago: Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” ArXiv, n.d. ieee: A. Biniaz et al., “Token swapping on trees,” arXiv. . ista: Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981. mla: Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981. short: A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.). date_created: 2020-06-08T12:25:25Z date_published: 2019-03-16T00:00:00Z date_updated: 2024-01-04T12:42:08Z day: '16' department: - _id: HeEd - _id: UlWa - _id: KrCh external_id: arxiv: - '1903.06981' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.06981 month: '03' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted related_material: record: - id: '7944' relation: dissertation_contains status: public - id: '12833' relation: later_version status: public status: public title: Token swapping on trees type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6418' abstract: - lang: eng text: Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general. acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: William J full_name: Gammerdinger, William J id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87 last_name: Gammerdinger orcid: 0000-0001-9638-1220 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053 apa: Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053 chicago: Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053. ieee: A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019. ista: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044. mla: Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053. short: A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044. date_created: 2019-05-13T07:58:38Z date_published: 2019-04-01T00:00:00Z date_updated: 2024-02-21T12:45:41Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evz053 ec_funded: 1 external_id: isi: - '000476569800003' file: - access_level: open_access checksum: 7d0ede297b6741f3dc89cd59017c7642 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:29:38Z date_updated: 2020-07-14T12:47:29Z file_id: '6446' file_name: 2019_GBE_Huylmans.pdf file_size: 1256303 relation: main_file file_date_updated: 2020-07-14T12:47:29Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1033-1044 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Genome biology and evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '6060' relation: popular_science status: public scopus_import: '1' status: public title: Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome 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: 11 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: '7154' article_processing_charge: No author: - first_name: Ruslan full_name: Guseinov, Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 citation: ama: Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154 apa: Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154 chicago: Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154. ieee: R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019. ista: Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154. mla: Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154. short: R. Guseinov, (2019). contributor: - first_name: Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 - first_name: Connor last_name: McMahan - first_name: Jesus id: 2DC83906-F248-11E8-B48F-1D18A9856A87 last_name: Perez Rodriguez - first_name: Chiara last_name: Daraio - first_name: Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 date_created: 2019-12-09T07:52:46Z date_published: 2019-12-06T00:00:00Z date_updated: 2024-02-21T12:45:03Z day: '06' ddc: - '000' department: - _id: BeBi doi: 10.15479/AT:ISTA:7154 ec_funded: 1 file: - access_level: open_access checksum: 155133e6e188e85b3c0676a5e70b9341 content_type: application/x-zip-compressed creator: dernst date_created: 2019-12-09T07:52:17Z date_updated: 2020-07-14T12:47:50Z file_id: '7155' file_name: temporal_morphing_supp_data.zip file_size: 65307107 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ month: '12' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publisher: Institute of Science and Technology Austria related_material: record: - id: '8433' relation: used_in_publication status: deleted - id: '7262' relation: used_in_publication status: public status: public title: Supplementary data for "Programming temporal morphing of self-actuated shells" tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6060' article_processing_charge: No author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060 apa: Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060 chicago: Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060. ieee: B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019. ista: Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060. mla: Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060. short: B. Vicoso, (2019). date_created: 2019-02-28T10:55:15Z date_published: 2019-02-28T00:00:00Z date_updated: 2024-02-21T12:45:42Z day: '28' department: - _id: BeVi doi: 10.15479/AT:ISTA:6060 file: - access_level: open_access checksum: a338a622d728af0e3199cb07e6dd64d3 content_type: application/zip creator: bvicoso date_created: 2019-02-28T10:54:27Z date_updated: 2020-07-14T12:47:17Z file_id: '6061' file_name: SupData.zip file_size: 36646050 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '6418' relation: research_paper status: public status: public title: 'Supplementary data for "Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). ' type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6074' abstract: - lang: eng text: "This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS." article_processing_charge: No author: - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074 apa: Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074 chicago: Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074. ieee: C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019. ista: Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074. mla: Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074. short: C. Dotter, G. Novarino, (2019). date_created: 2019-03-07T13:32:35Z date_published: 2019-01-09T00:00:00Z date_updated: 2024-02-21T13:41:01Z day: '09' ddc: - '570' department: - _id: GaNo doi: 10.15479/AT:ISTA:6074 file: - access_level: open_access checksum: bc1b285edca9e98a2c63d153c79bb75b content_type: application/zip creator: dernst date_created: 2019-03-07T13:37:19Z date_updated: 2020-07-14T12:47:18Z file_id: '6084' file_name: Setd5_paper.zip file_size: 33202743 relation: supplementary_material file_date_updated: 2020-07-14T12:47:18Z has_accepted_license: '1' month: '01' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '3' relation: research_paper status: public status: public title: Supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition" type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6062' abstract: - lang: eng text: Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7). article_processing_charge: No author: - first_name: Michele full_name: Nardin, Michele id: 30BD0376-F248-11E8-B48F-1D18A9856A87 last_name: Nardin orcid: 0000-0001-8849-6570 citation: ama: Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062 apa: Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062 chicago: Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062. ieee: M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. ista: Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062. mla: Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062. short: M. Nardin, (2019). date_created: 2019-03-04T14:20:58Z date_published: 2019-03-29T00:00:00Z date_updated: 2024-02-21T12:46:04Z day: '29' department: - _id: JoCs doi: 10.15479/AT:ISTA:6062 file: - access_level: open_access checksum: 48e7b9a02939b763417733239522a236 content_type: application/zip creator: mnardin date_created: 2019-03-05T09:29:37Z date_updated: 2020-07-14T12:47:18Z file_id: '6068' file_name: Online_data.zip file_size: 37002186 relation: main_file title: Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals" file_date_updated: 2020-07-14T12:47:18Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '6194' relation: research_paper status: public status: public title: Supplementary Code and Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals" tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6089' abstract: - lang: eng text: Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246 apa: Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246 chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246. ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019. ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515. mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246. short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515. date_created: 2019-03-10T22:59:19Z date_published: 2019-03-01T00:00:00Z date_updated: 2024-02-21T13:59:17Z day: '01' department: - _id: BeVi - _id: NiBa doi: 10.1093/molbev/msy246 external_id: isi: - '000462585100006' pmid: - '30590559' intvolume: ' 36' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30590559 month: '03' oa: 1 oa_version: Submitted Version page: 500-515 pmid: 1 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Molecular biology and evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '5757' relation: popular_science status: public scopus_import: '1' status: public title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 36 year: '2019' ... --- _id: '6179' abstract: - lang: eng text: "In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: 'Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179' apa: 'Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179' chicago: 'Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179.' ieee: 'D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.' ista: 'Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.' mla: 'Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.' short: 'D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019.' date_created: 2019-03-28T08:58:59Z date_published: 2019-03-18T00:00:00Z date_updated: 2024-02-22T14:34:33Z day: '18' ddc: - '515' - '519' degree_awarded: PhD department: - _id: LaEr doi: 10.15479/AT:ISTA:th6179 ec_funded: 1 file: - access_level: closed checksum: 6926f66f28079a81c4937e3764be00fc content_type: application/x-gzip creator: dernst date_created: 2019-03-28T08:53:52Z date_updated: 2020-07-14T12:47:21Z file_id: '6180' file_name: 2019_Schroeder_Thesis.tar.gz file_size: 7104482 relation: source_file - access_level: open_access checksum: 7d0ebb8d1207e89768cdd497a5bf80fb content_type: application/pdf creator: dernst date_created: 2019-03-28T08:53:52Z date_updated: 2020-07-14T12:47:21Z file_id: '6181' file_name: 2019_Schroeder_Thesis.pdf file_size: 4228794 relation: main_file file_date_updated: 2020-07-14T12:47:21Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '375' project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1144' relation: part_of_dissertation status: public - id: '6186' relation: part_of_dissertation status: public - id: '6185' relation: part_of_dissertation status: public - id: '6182' relation: part_of_dissertation status: public - id: '1012' relation: part_of_dissertation status: public - id: '6184' relation: part_of_dissertation status: public status: public supervisor: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 title: 'From Dyson to Pearcey: Universal statistics in random matrix theory' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '6482' abstract: - lang: eng text: 'Computer vision systems for automatic image categorization have become accurate and reliable enough that they can run continuously for days or even years as components of real-world commercial applications. A major open problem in this context, however, is quality control. Good classification performance can only be expected if systems run under the specific conditions, in particular data distributions, that they were trained for. Surprisingly, none of the currently used deep network architectures have a built-in functionality that could detect if a network operates on data from a distribution it was not trained for, such that potentially a warning to the human users could be triggered. In this work, we describe KS(conf), a procedure for detecting such outside of specifications (out-of-specs) operation, based on statistical testing of the network outputs. We show by extensive experiments using the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that KS(conf) reliably detects out-of-specs situations. It furthermore has a number of properties that make it a promising candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with all networks, including pretrained ones, and requires no a priori knowledge of how the data distribution could change. ' alternative_title: - LNCS article_processing_charge: No author: - first_name: Rémy full_name: Sun, Rémy last_name: Sun - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18' apa: 'Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-12939-2_18' chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-12939-2_18.' ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.' ista: 'Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS, vol. 11269, 244–259.' mla: 'Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:10.1007/978-3-030-12939-2_18.' short: R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259. conference: end_date: 2018-10-12 location: Stuttgart, Germany name: 'GCPR: Conference on Pattern Recognition' start_date: 2018-10-09 date_created: 2019-05-24T09:48:36Z date_published: 2019-02-14T00:00:00Z date_updated: 2024-02-22T14:57:29Z day: '14' department: - _id: ChLa doi: 10.1007/978-3-030-12939-2_18 ec_funded: 1 external_id: arxiv: - '1804.04171' intvolume: ' 11269' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.04171 month: '02' oa: 1 oa_version: Preprint page: 244-259 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: eissn: - 1611-3349 isbn: - '9783030129385' - '9783030129392' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '6944' relation: later_version status: public scopus_import: '1' status: public title: 'KS(conf): A light-weight test if a ConvNet operates outside of Its specifications' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11269 year: '2019' ... --- _id: '6642' abstract: - lang: eng text: We present a thermodynamically based approach to the design of models for viscoelastic fluids with stress diffusion effect. In particular, we show how to add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus, FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that the resulting models with the added stress diffusion term are thermodynamically consistent in the sense that they obey the first and the second law of thermodynamics. We point out the potential applications of the provided thermodynamical background in the study of flows of fluids described by the proposed models. article_number: '020002' article_processing_charge: No author: - first_name: Mark full_name: Dostalík, Mark last_name: Dostalík - first_name: Vít full_name: Pruša, Vít last_name: Pruša - first_name: Tomas full_name: Skrivan, Tomas id: 486A5A46-F248-11E8-B48F-1D18A9856A87 last_name: Skrivan citation: ama: 'Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing; 2019. doi:10.1063/1.5109493' apa: 'Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of some classical viscoelastic rate-type models. In AIP Conference Proceedings (Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493' chicago: Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings, Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493. ieee: M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech Republic, 2019, vol. 2107. ista: Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference on Novel Trends in Rheology vol. 2107, 020002. mla: Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing, 2019, doi:10.1063/1.5109493. short: M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019. conference: end_date: 2019-07-31 location: Zlin, Czech Republic name: 8th International Conference on Novel Trends in Rheology start_date: 2019-07-30 date_created: 2019-07-15T10:07:09Z date_published: 2019-05-21T00:00:00Z date_updated: 2024-02-28T13:01:28Z day: '21' department: - _id: ChWo doi: 10.1063/1.5109493 external_id: arxiv: - '1902.07983' isi: - '000479303100002' intvolume: ' 2107' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07983 month: '05' oa: 1 oa_version: Preprint publication: AIP Conference Proceedings publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: On diffusive variants of some classical viscoelastic rate-type models type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2107 year: '2019' ... --- _id: '7226' article_number: '123504' article_processing_charge: No article_type: letter_note author: - first_name: Vojkan full_name: Jaksic, Vojkan last_name: Jaksic - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 2019;60(12). doi:10.1063/1.5138135' apa: 'Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.5138135' chicago: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135.' ieee: 'V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics, vol. 60, no. 12. AIP Publishing, 2019.' ista: 'Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.' mla: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.' short: V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019). date_created: 2020-01-05T23:00:46Z date_published: 2019-12-01T00:00:00Z date_updated: 2024-02-28T13:01:45Z day: '01' ddc: - '500' department: - _id: RoSe doi: 10.1063/1.5138135 external_id: isi: - '000505529800002' file: - access_level: open_access checksum: bbd12ad1999a9ad7ba4d3c6f2e579c22 content_type: application/pdf creator: dernst date_created: 2020-01-07T14:59:13Z date_updated: 2020-07-14T12:47:54Z file_id: '7244' file_name: 2019_JournalMathPhysics_Jaksic.pdf file_size: 1025015 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 60' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Journal of Mathematical Physics publication_identifier: issn: - '00222488' publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2019' ... --- _id: '7190' abstract: - lang: eng text: We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas. article_number: '033177' article_processing_charge: No article_type: original author: - first_name: D. full_name: Huber, D. last_name: Huber - first_name: H.-W. full_name: Hammer, H.-W. last_name: Hammer - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177 apa: Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177 chicago: Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research. American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177. ieee: D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” Physical Review Research, vol. 1, no. 3. American Physical Society, 2019. ista: Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177. mla: Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:10.1103/physrevresearch.1.033177. short: D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019). date_created: 2019-12-17T13:03:41Z date_published: 2019-12-16T00:00:00Z date_updated: 2024-02-28T13:11:40Z day: '16' ddc: - '530' department: - _id: MiLe doi: 10.1103/physrevresearch.1.033177 ec_funded: 1 external_id: arxiv: - '1908.02483' file: - access_level: open_access checksum: 382eb67e62a77052a23887332d363f96 content_type: application/pdf creator: dernst date_created: 2019-12-18T07:13:14Z date_updated: 2020-07-14T12:47:52Z file_id: '7193' file_name: 2019_PhysRevResearch_Huber.pdf file_size: 1370022 relation: main_file file_date_updated: 2020-07-14T12:47:52Z has_accepted_license: '1' intvolume: ' 1' issue: '3' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Research publication_identifier: issn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas 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: 1 year: '2019' ... --- _id: '6575' abstract: - lang: eng text: Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit. article_number: '220603' article_processing_charge: No article_type: original author: - first_name: Soonwon full_name: Choi, Soonwon last_name: Choi - first_name: Christopher J. full_name: Turner, Christopher J. last_name: Turner - first_name: Hannes full_name: Pichler, Hannes last_name: Pichler - first_name: Wen Wei full_name: Ho, Wen Wei last_name: Ho - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Mikhail D. full_name: Lukin, Mikhail D. last_name: Lukin - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin citation: ama: Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603 apa: Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z., … Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603 chicago: Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603. ieee: S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society, 2019. ista: Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 122(22), 220603. mla: Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.220603. short: S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn, M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019). date_created: 2019-06-23T21:59:13Z date_published: 2019-06-07T00:00:00Z date_updated: 2024-02-28T13:12:22Z day: '07' department: - _id: MaSe doi: 10.1103/PhysRevLett.122.220603 external_id: arxiv: - '1812.05561' isi: - '000470885800005' intvolume: ' 122' isi: 1 issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1812.05561 month: '06' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: eissn: - '10797114' issn: - '00319007' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Emergent SU(2) dynamics and perfect quantum many-body scars type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2019' ... --- _id: '6092' abstract: - lang: eng text: In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales. article_number: '064428' article_processing_charge: No author: - first_name: Johann H full_name: Mentink, Johann H last_name: Mentink - first_name: Mikhail full_name: Katsnelson, Mikhail last_name: Katsnelson - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428 apa: Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.99.064428 chicago: Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428. ieee: J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American Physical Society, 2019. ista: Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428. mla: Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society, 2019, doi:10.1103/PhysRevB.99.064428. short: J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019). date_created: 2019-03-10T22:59:20Z date_published: 2019-02-01T00:00:00Z date_updated: 2024-02-28T13:11:54Z day: '01' department: - _id: MiLe doi: 10.1103/PhysRevB.99.064428 external_id: arxiv: - '1802.01638' isi: - '000459223400004' intvolume: ' 99' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.01638 month: '02' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review B publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Quantum many-body dynamics of the Einstein-de Haas effect type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2019' ... --- _id: '6090' abstract: - lang: eng text: Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing. article_number: '022423' article_processing_charge: No author: - first_name: Martín full_name: Carballo-Pacheco, Martín last_name: Carballo-Pacheco - first_name: Jonathan full_name: Desponds, Jonathan last_name: Desponds - first_name: Tatyana full_name: Gavrilchenko, Tatyana last_name: Gavrilchenko - first_name: Andreas full_name: Mayer, Andreas last_name: Mayer - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Gautam full_name: Reddy, Gautam last_name: Reddy - first_name: Ilya full_name: Nemenman, Ilya last_name: Nemenman - first_name: Thierry full_name: Mora, Thierry last_name: Mora citation: ama: Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423 apa: Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423 chicago: Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423. ieee: M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019. ista: Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423. mla: Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423. short: M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019). date_created: 2019-03-10T22:59:20Z date_published: 2019-02-26T00:00:00Z date_updated: 2024-02-28T13:12:06Z day: '26' department: - _id: NiBa - _id: GaTk doi: 10.1103/PhysRevE.99.022423 external_id: isi: - '000459916500007' intvolume: ' 99' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/448118v1.abstract month: '02' oa: 1 oa_version: Preprint publication: Physical Review E publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Receptor crosstalk improves concentration sensing of multiple ligands type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2019' ... --- _id: '6786' abstract: - lang: eng text: Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations. article_number: '021026' article_processing_charge: No article_type: original author: - first_name: Colin full_name: Hubert, Colin last_name: Hubert - first_name: Yifat full_name: Baruchi, Yifat last_name: Baruchi - first_name: Yotam full_name: Mazuz-Harpaz, Yotam last_name: Mazuz-Harpaz - first_name: Kobi full_name: Cohen, Kobi last_name: Cohen - first_name: Klaus full_name: Biermann, Klaus last_name: Biermann - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Ken full_name: West, Ken last_name: West - first_name: Loren full_name: Pfeiffer, Loren last_name: Pfeiffer - first_name: Ronen full_name: Rapaport, Ronen last_name: Rapaport - first_name: Paulo full_name: Santos, Paulo last_name: Santos citation: ama: Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026 apa: Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026 chicago: Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026. ieee: C. Hubert et al., “Attractive dipolar coupling between stacked exciton fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019. ista: Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026. mla: Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:10.1103/PhysRevX.9.021026. short: C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019). date_created: 2019-08-11T21:59:20Z date_published: 2019-05-08T00:00:00Z date_updated: 2024-02-28T13:12:48Z day: '08' ddc: - '530' department: - _id: MiLe doi: 10.1103/PhysRevX.9.021026 external_id: arxiv: - '1807.11238' isi: - '000467402900001' file: - access_level: open_access checksum: 065ff82ee4a1d2c3773ce4b76ff4213c content_type: application/pdf creator: dernst date_created: 2019-08-12T12:14:18Z date_updated: 2020-07-14T12:47:40Z file_id: '6802' file_name: 2019_PhysReviewX_Hubert.pdf file_size: 1193550 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review X publication_identifier: eissn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Attractive dipolar coupling between stacked exciton fluids 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: 9 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 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: '7200' abstract: - lang: eng text: Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario). article_number: '174518' article_processing_charge: No article_type: original author: - first_name: Pietro full_name: Brighi, Pietro id: 4115AF5C-F248-11E8-B48F-1D18A9856A87 last_name: Brighi orcid: 0000-0002-7969-2729 - first_name: Marco full_name: Grilli, Marco last_name: Grilli - first_name: Brigitte full_name: Leridon, Brigitte last_name: Leridon - first_name: Sergio full_name: Caprara, Sergio last_name: Caprara citation: ama: Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518 apa: Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518 chicago: Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.100.174518. ieee: P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” Physical Review B, vol. 100, no. 17. American Physical Society, 2019. ista: Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518. mla: Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518. short: P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019). date_created: 2019-12-22T23:00:41Z date_published: 2019-11-25T00:00:00Z date_updated: 2024-02-28T13:14:08Z day: '25' department: - _id: MaSe doi: 10.1103/PhysRevB.100.174518 external_id: arxiv: - '1907.13579' isi: - '000498845700006' intvolume: ' 100' isi: 1 issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.13579 month: '11' 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: Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2019' ... --- _id: '6779' abstract: - lang: eng text: "Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace." article_number: '013112' article_processing_charge: No article_type: original author: - first_name: Balachandra full_name: Suri, Balachandra id: 47A5E706-F248-11E8-B48F-1D18A9856A87 last_name: Suri - first_name: Ravi Kumar full_name: Pallantla, Ravi Kumar last_name: Pallantla - first_name: Michael F. full_name: Schatz, Michael F. last_name: Schatz - first_name: Roman O. full_name: Grigoriev, Roman O. last_name: Grigoriev citation: ama: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112 apa: Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112 chicago: Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112. ieee: B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, vol. 100, no. 1. American Physical Society, 2019. ista: Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112. mla: Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112. short: B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019). date_created: 2019-08-09T09:40:41Z date_published: 2019-07-25T00:00:00Z date_updated: 2024-02-28T13:13:00Z day: '25' ddc: - '532' department: - _id: BjHo doi: 10.1103/physreve.100.013112 ec_funded: 1 external_id: arxiv: - '1907.05860' isi: - '000477911800012' intvolume: ' 100' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.05860 month: '07' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Heteroclinic and homoclinic connections in a Kolmogorov-like flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 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 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: '7145' abstract: - lang: eng text: End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information. article_number: '205412' article_processing_charge: No article_type: original author: - first_name: G. L. R. full_name: Anselmetti, G. L. R. last_name: Anselmetti - first_name: E. A. full_name: Martinez, E. A. last_name: Martinez - first_name: G. C. full_name: Ménard, G. C. last_name: Ménard - first_name: D. full_name: Puglia, D. last_name: Puglia - first_name: F. K. full_name: Malinowski, F. K. last_name: Malinowski - first_name: J. S. full_name: Lee, J. S. last_name: Lee - first_name: S. full_name: Choi, S. last_name: Choi - first_name: M. full_name: Pendharkar, M. last_name: Pendharkar - first_name: C. J. full_name: Palmstrøm, C. J. last_name: Palmstrøm - first_name: C. M. full_name: Marcus, C. M. last_name: Marcus - first_name: L. full_name: Casparis, L. last_name: Casparis - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412 apa: Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.205412 chicago: Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412. ieee: G. L. R. Anselmetti et al., “End-to-end correlated subgap states in hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical Society, 2019. ista: Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412. mla: Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:10.1103/physrevb.100.205412. short: G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019). date_created: 2019-12-04T16:02:25Z date_published: 2019-11-15T00:00:00Z date_updated: 2024-02-28T13:13:51Z day: '15' department: - _id: AnHi doi: 10.1103/physrevb.100.205412 external_id: arxiv: - '1908.05549' isi: - '000495967500006' intvolume: ' 100' isi: 1 issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.05549 month: '11' 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: End-to-end correlated subgap states in hybrid nanowires type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2019' ...