--- _id: '10748' abstract: - lang: eng text: The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based superconducting rings is valuable for characterizing the basic properties of the superconductor, and may also provide important insight into the superconducting paring symmetry. We report the fabrications of micron-sized rings and disks from thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid states in rings we developed a custom-tailored version of magnetic force microscopy (MFM). This technique has a number of qualitative advantages for working with mesoscopic superconducting samples in comparison to the conventional MFM and other imaging techniques. We observed metastable fluxoid states in rings of different sizes. Thermally activated fluxoid dynamics of these states was studied and modeled. In addition, we found different regimes of interaction between Fe(Se, Te) ring and MFM tip which are explained. Possibilities of the existence of exotic vortex states and proposals for experiments to test the symmetry of the superconducting order parameter in iron based superconductors are analyzed. alternative_title: - Bulletin of the American Physical Society article_number: G16.00009 article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Can full_name: Zhang, Can last_name: Zhang - first_name: Tyler full_name: Naibert, Tyler last_name: Naibert - first_name: James full_name: Eckstein, James last_name: Eckstein - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian citation: ama: 'Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In: APS March Meeting 2015. Vol 60. American Physical Society; 2015.' apa: 'Polshyn, H., Zhang, C., Naibert, T., Eckstein, J., & Budakian, R. (2015). Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In APS March Meeting 2015 (Vol. 60). San Antonio, TX, United States: American Physical Society.' chicago: Polshyn, Hryhoriy, Can Zhang, Tyler Naibert, James Eckstein, and Raffi Budakian. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” In APS March Meeting 2015, Vol. 60. American Physical Society, 2015. ieee: H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, and R. Budakian, “Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy,” in APS March Meeting 2015, San Antonio, TX, United States, 2015, vol. 60, no. 1. ista: 'Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. 2015. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. APS March Meeting 2015. APS: American Physical Society, Bulletin of the American Physical Society, vol. 60, G16.00009.' mla: Polshyn, Hryhoriy, et al. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” APS March Meeting 2015, vol. 60, no. 1, G16.00009, American Physical Society, 2015. short: H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, R. Budakian, in:, APS March Meeting 2015, American Physical Society, 2015. conference: end_date: 2015-03-06 location: San Antonio, TX, United States name: 'APS: American Physical Society' start_date: 2015-03-02 date_created: 2022-02-08T10:17:09Z date_published: 2015-03-01T00:00:00Z date_updated: 2022-02-08T10:42:53Z day: '01' extern: '1' intvolume: ' 60' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR15/Event/238442 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2015 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 60 year: '2015' ... --- _id: '10794' abstract: - lang: eng text: Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation. acknowledgement: "The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX." article_number: '42' article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Parise, Francesca last_name: Parise - first_name: John full_name: Lygeros, John last_name: Lygeros - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 citation: ama: 'Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042' apa: 'Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042' chicago: 'Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.' ieee: 'F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015.' ista: 'Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.' mla: 'Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.' short: F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015). date_created: 2022-02-25T11:42:25Z date_published: 2015-06-10T00:00:00Z date_updated: 2022-02-25T11:59:23Z day: '10' ddc: - '000' - '570' department: - _id: ToHe - _id: GaTk doi: 10.3389/fenvs.2015.00042 ec_funded: 1 file: - access_level: open_access checksum: 26c222487564e1be02a11d688d6f769d content_type: application/pdf creator: dernst date_created: 2022-02-25T11:55:26Z date_updated: 2022-02-25T11:55:26Z file_id: '10795' file_name: 2015_FrontiersEnvironmScience_Parise.pdf file_size: 1371201 relation: main_file success: 1 file_date_updated: 2022-02-25T11:55:26Z has_accepted_license: '1' intvolume: ' 3' keyword: - General Environmental Science language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Frontiers in Environmental Science publication_identifier: issn: - 2296-665X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study' 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: 3 year: '2015' ... --- _id: '10796' abstract: - lang: eng text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).' acknowledgement: "The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award." article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 citation: ama: 'Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029. doi:10.1137/1.9781611973730.69' apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69' chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29. SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69. ieee: K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029. ista: 'Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029.' mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69. short: K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029. conference: end_date: 2015-01-06 location: San Diego, CA, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2015-01-04 date_created: 2022-02-25T12:18:43Z date_published: 2015-01-01T00:00:00Z date_updated: 2022-02-25T12:33:32Z day: '01' department: - _id: KrCh doi: 10.1137/1.9781611973730.69 ec_funded: 1 external_id: arxiv: - '1409.6690' intvolume: ' 2015' issue: '1' language: - iso: eng month: '01' oa_version: Preprint page: 1018-1029 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: isbn: - 978-161197374-7 publication_status: published publisher: SIAM quality_controlled: '1' scopus_import: '1' status: public title: The value 1 problem under finite-memory strategies for concurrent mean-payoff games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015 year: '2015' ... --- _id: '1106' abstract: - lang: eng text: Circumferential skin creases Kunze type (CSC-KT) is a specific congenital entity with an unknown genetic cause. The disease phenotype comprises characteristic circumferential skin creases accompanied by intellectual disability, a cleft palate, short stature, and dysmorphic features. Here, we report that mutations in either MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a member of the microtubule end-binding family of proteins that bind to the guanosine triphosphate cap at growing microtubule plus ends, and TUBB encodes a β-tubulin isotype that is expressed abundantly in the developing brain. Functional analyses of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer folding and assembly pathway that leads to a compromised yield of native heterodimers. The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we show that the mutations result in enhanced MAPRE2 binding to microtubules, implying an increased dwell time at microtubule plus ends. Further, in vivo analysis of MAPRE2 mutations in a zebrafish model of craniofacial development shows that the variants most likely perturb the patterning of branchial arches, either through excessive activity (under a recessive paradigm) or through haploinsufficiency (dominant de novo paradigm). Taken together, our data add CSC-KT to the growing list of tubulinopathies and highlight how multiple inheritance paradigms can affect dosage-sensitive biological systems so as to result in the same clinical defect. author: - first_name: Mala full_name: Isrie, Mala last_name: Isrie - first_name: Martin full_name: Breuss, Martin last_name: Breuss - first_name: Guoling full_name: Tian, Guoling last_name: Tian - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Francesca full_name: Cristofoli, Francesca last_name: Cristofoli - first_name: Jasmin full_name: Morandell, Jasmin id: 4739D480-F248-11E8-B48F-1D18A9856A87 last_name: Morandell - first_name: Zachari A full_name: Kupchinsky, Zachari A last_name: Kupchinsky - first_name: Alejandro full_name: Sifrim, Alejandro last_name: Sifrim - first_name: Celia full_name: Rodriguez Rodriguez, Celia last_name: Rodriguez Rodriguez - first_name: Elena P full_name: Dapena, Elena P last_name: Dapena - first_name: Kurston full_name: Doonanco, Kurston last_name: Doonanco - first_name: Norma full_name: Leonard, Norma last_name: Leonard - first_name: Faten full_name: Tinsa, Faten last_name: Tinsa - first_name: Stéphanie full_name: Moortgat, Stéphanie last_name: Moortgat - first_name: Hakan full_name: Ulucan, Hakan last_name: Ulucan - first_name: Erkan full_name: Koparir, Erkan last_name: Koparir - first_name: Ender full_name: Karaca, Ender last_name: Karaca - first_name: Nicholas full_name: Katsanis, Nicholas last_name: Katsanis - first_name: Valeria full_name: Marton, Valeria last_name: Marton - first_name: Joris R full_name: Vermeesch, Joris R last_name: Vermeesch - first_name: Erica E full_name: Davis, Erica E last_name: Davis - first_name: Nicholas J full_name: Cowan, Nicholas J last_name: Cowan - first_name: David full_name: Keays, David last_name: Keays - first_name: Hilde full_name: Van Esch, Hilde last_name: Van Esch citation: ama: Isrie M, Breuss M, Tian G, et al. Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type. The American Journal of Human Genetics. 2015;97(6):790-800. doi:10.1016/j.ajhg.2015.10.014 apa: Isrie, M., Breuss, M., Tian, G., Hansen, A. H., Cristofoli, F., Morandell, J., … Van Esch, H. (2015). Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type. The American Journal of Human Genetics. Cell Press. https://doi.org/10.1016/j.ajhg.2015.10.014 chicago: Isrie, Mala, Martin Breuss, Guoling Tian, Andi H Hansen, Francesca Cristofoli, Jasmin Morandell, Zachari A Kupchinsky, et al. “Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.” The American Journal of Human Genetics. Cell Press, 2015. https://doi.org/10.1016/j.ajhg.2015.10.014. ieee: M. Isrie et al., “Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type,” The American Journal of Human Genetics, vol. 97, no. 6. Cell Press, pp. 790–800, 2015. ista: Isrie M, Breuss M, Tian G, Hansen AH, Cristofoli F, Morandell J, Kupchinsky ZA, Sifrim A, Rodriguez Rodriguez C, Dapena EP, Doonanco K, Leonard N, Tinsa F, Moortgat S, Ulucan H, Koparir E, Karaca E, Katsanis N, Marton V, Vermeesch JR, Davis EE, Cowan NJ, Keays D, Van Esch H. 2015. Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type. The American Journal of Human Genetics. 97(6), 790–800. mla: Isrie, Mala, et al. “Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.” The American Journal of Human Genetics, vol. 97, no. 6, Cell Press, 2015, pp. 790–800, doi:10.1016/j.ajhg.2015.10.014. short: M. Isrie, M. Breuss, G. Tian, A.H. Hansen, F. Cristofoli, J. Morandell, Z.A. Kupchinsky, A. Sifrim, C. Rodriguez Rodriguez, E.P. Dapena, K. Doonanco, N. Leonard, F. Tinsa, S. Moortgat, H. Ulucan, E. Koparir, E. Karaca, N. Katsanis, V. Marton, J.R. Vermeesch, E.E. Davis, N.J. Cowan, D. Keays, H. Van Esch, The American Journal of Human Genetics 97 (2015) 790–800. date_created: 2018-12-11T11:50:11Z date_published: 2015-12-03T00:00:00Z date_updated: 2021-01-12T06:48:19Z day: '03' doi: 10.1016/j.ajhg.2015.10.014 extern: '1' intvolume: ' 97' issue: '6' language: - iso: eng month: '12' oa_version: None page: 790 - 800 publication: The American Journal of Human Genetics publication_status: published publisher: Cell Press publist_id: '6264' quality_controlled: '1' status: public title: Mutations in either TUBB or MAPRE2 cause circumferential skin creases Kunze type type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2015' ... --- _id: '11079' abstract: - lang: eng text: Aging is a major risk factor for many human diseases, and in vitro generation of human neurons is an attractive approach for modeling aging-related brain disorders. However, modeling aging in differentiated human neurons has proved challenging. We generated neurons from human donors across a broad range of ages, either by iPSC-based reprogramming and differentiation or by direct conversion into induced neurons (iNs). While iPSCs and derived neurons did not retain aging-associated gene signatures, iNs displayed age-specific transcriptional profiles and revealed age-associated decreases in the nuclear transport receptor RanBP17. We detected an age-dependent loss of nucleocytoplasmic compartmentalization (NCC) in donor fibroblasts and corresponding iNs and found that reduced RanBP17 impaired NCC in young cells, while iPSC rejuvenation restored NCC in aged cells. These results show that iNs retain important aging-related signatures, thus allowing modeling of the aging process in vitro, and they identify impaired NCC as an important factor in human aging. article_processing_charge: No article_type: original author: - first_name: Jerome full_name: Mertens, Jerome last_name: Mertens - first_name: Apuã C.M. full_name: Paquola, Apuã C.M. last_name: Paquola - first_name: Manching full_name: Ku, Manching last_name: Ku - first_name: Emily full_name: Hatch, Emily last_name: Hatch - first_name: Lena full_name: Böhnke, Lena last_name: Böhnke - first_name: Shauheen full_name: Ladjevardi, Shauheen last_name: Ladjevardi - first_name: Sean full_name: McGrath, Sean last_name: McGrath - first_name: Benjamin full_name: Campbell, Benjamin last_name: Campbell - first_name: Hyungjun full_name: Lee, Hyungjun last_name: Lee - first_name: Joseph R. full_name: Herdy, Joseph R. last_name: Herdy - first_name: J. Tiago full_name: Gonçalves, J. Tiago last_name: Gonçalves - first_name: Tomohisa full_name: Toda, Tomohisa last_name: Toda - first_name: Yongsung full_name: Kim, Yongsung last_name: Kim - first_name: Jürgen full_name: Winkler, Jürgen last_name: Winkler - first_name: Jun full_name: Yao, Jun last_name: Yao - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Fred H. full_name: Gage, Fred H. last_name: Gage citation: ama: Mertens J, Paquola ACM, Ku M, et al. Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell Stem Cell. 2015;17(6):705-718. doi:10.1016/j.stem.2015.09.001 apa: Mertens, J., Paquola, A. C. M., Ku, M., Hatch, E., Böhnke, L., Ladjevardi, S., … Gage, F. H. (2015). Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2015.09.001 chicago: Mertens, Jerome, Apuã C.M. Paquola, Manching Ku, Emily Hatch, Lena Böhnke, Shauheen Ladjevardi, Sean McGrath, et al. “Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects.” Cell Stem Cell. Elsevier, 2015. https://doi.org/10.1016/j.stem.2015.09.001. ieee: J. Mertens et al., “Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects,” Cell Stem Cell, vol. 17, no. 6. Elsevier, pp. 705–718, 2015. ista: Mertens J, Paquola ACM, Ku M, Hatch E, Böhnke L, Ladjevardi S, McGrath S, Campbell B, Lee H, Herdy JR, Gonçalves JT, Toda T, Kim Y, Winkler J, Yao J, Hetzer M, Gage FH. 2015. Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell Stem Cell. 17(6), 705–718. mla: Mertens, Jerome, et al. “Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects.” Cell Stem Cell, vol. 17, no. 6, Elsevier, 2015, pp. 705–18, doi:10.1016/j.stem.2015.09.001. short: J. Mertens, A.C.M. Paquola, M. Ku, E. Hatch, L. Böhnke, S. Ladjevardi, S. McGrath, B. Campbell, H. Lee, J.R. Herdy, J.T. Gonçalves, T. Toda, Y. Kim, J. Winkler, J. Yao, M. Hetzer, F.H. Gage, Cell Stem Cell 17 (2015) 705–718. date_created: 2022-04-07T07:49:51Z date_published: 2015-12-03T00:00:00Z date_updated: 2022-07-18T08:44:21Z day: '03' doi: 10.1016/j.stem.2015.09.001 extern: '1' external_id: pmid: - '26456686' intvolume: ' 17' issue: '6' keyword: - Cell Biology - Genetics - Molecular Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.stem.2015.09.001 month: '12' oa: 1 oa_version: Published Version page: 705-718 pmid: 1 publication: Cell Stem Cell publication_identifier: issn: - 1934-5909 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 17 year: '2015' ... --- _id: '11077' abstract: - lang: eng text: Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that mediate nuclear transport across the nuclear envelope. Recent evidence suggests that several Nups have additional roles in controlling the activation and silencing of developmental genes; however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the derepression of developmental genes and induction of early differentiation. This loss of stem cell identity is not associated with defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds around the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its target loci. Our results demonstrate a chromatin-associated role of Nup153 in maintaining stem cell pluripotency by functioning in mammalian epigenetic gene silencing. article_processing_charge: No article_type: original author: - first_name: Filipe V. full_name: Jacinto, Filipe V. last_name: Jacinto - first_name: Chris full_name: Benner, Chris last_name: Benner - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Jacinto FV, Benner C, Hetzer M. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes & Development. 2015;29(12):1224-1238. doi:10.1101/gad.260919.115 apa: Jacinto, F. V., Benner, C., & Hetzer, M. (2015). The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.260919.115 chicago: Jacinto, Filipe V., Chris Benner, and Martin Hetzer. “The Nucleoporin Nup153 Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” Genes & Development. Cold Spring Harbor Laboratory, 2015. https://doi.org/10.1101/gad.260919.115. ieee: F. V. Jacinto, C. Benner, and M. Hetzer, “The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing,” Genes & Development, vol. 29, no. 12. Cold Spring Harbor Laboratory, pp. 1224–1238, 2015. ista: Jacinto FV, Benner C, Hetzer M. 2015. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes & Development. 29(12), 1224–1238. mla: Jacinto, Filipe V., et al. “The Nucleoporin Nup153 Regulates Embryonic Stem Cell Pluripotency through Gene Silencing.” Genes & Development, vol. 29, no. 12, Cold Spring Harbor Laboratory, 2015, pp. 1224–38, doi:10.1101/gad.260919.115. short: F.V. Jacinto, C. Benner, M. Hetzer, Genes & Development 29 (2015) 1224–1238. date_created: 2022-04-07T07:49:31Z date_published: 2015-06-16T00:00:00Z date_updated: 2022-07-18T08:43:51Z day: '16' doi: 10.1101/gad.260919.115 extern: '1' external_id: pmid: - '26080816' intvolume: ' 29' issue: '12' keyword: - Developmental Biology - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/gad.260919.115 month: '06' oa: 1 oa_version: Published Version page: 1224-1238 pmid: 1 publication: Genes & Development publication_identifier: eissn: - 1549-5477 issn: - 0890-9369 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 29 year: '2015' ... --- _id: '11078' abstract: - lang: eng text: Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats. article_processing_charge: No article_type: original author: - first_name: Alessandro full_name: Ori, Alessandro last_name: Ori - first_name: Brandon H. full_name: Toyama, Brandon H. last_name: Toyama - first_name: Michael S. full_name: Harris, Michael S. last_name: Harris - first_name: Thomas full_name: Bock, Thomas last_name: Bock - first_name: Murat full_name: Iskar, Murat last_name: Iskar - first_name: Peer full_name: Bork, Peer last_name: Bork - first_name: Nicholas T. full_name: Ingolia, Nicholas T. last_name: Ingolia - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Martin full_name: Beck, Martin last_name: Beck citation: ama: Ori A, Toyama BH, Harris MS, et al. Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats. Cell Systems. 2015;1(3):P224-237. doi:10.1016/j.cels.2015.08.012 apa: Ori, A., Toyama, B. H., Harris, M. S., Bock, T., Iskar, M., Bork, P., … Beck, M. (2015). Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats. Cell Systems. Elsevier. https://doi.org/10.1016/j.cels.2015.08.012 chicago: Ori, Alessandro, Brandon H. Toyama, Michael S. Harris, Thomas Bock, Murat Iskar, Peer Bork, Nicholas T. Ingolia, Martin Hetzer, and Martin Beck. “Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.” Cell Systems. Elsevier, 2015. https://doi.org/10.1016/j.cels.2015.08.012. ieee: A. Ori et al., “Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats,” Cell Systems, vol. 1, no. 3. Elsevier, pp. P224-237, 2015. ista: Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer M, Beck M. 2015. Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats. Cell Systems. 1(3), P224-237. mla: Ori, Alessandro, et al. “Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.” Cell Systems, vol. 1, no. 3, Elsevier, 2015, pp. P224-237, doi:10.1016/j.cels.2015.08.012. short: A. Ori, B.H. Toyama, M.S. Harris, T. Bock, M. Iskar, P. Bork, N.T. Ingolia, M. Hetzer, M. Beck, Cell Systems 1 (2015) P224-237. date_created: 2022-04-07T07:49:39Z date_published: 2015-09-23T00:00:00Z date_updated: 2022-07-18T08:44:07Z day: '23' doi: 10.1016/j.cels.2015.08.012 extern: '1' external_id: pmid: - '27135913' intvolume: ' 1' issue: '3' keyword: - Cell Biology - Histology - Pathology and Forensic Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cels.2015.08.012 month: '09' oa: 1 oa_version: Published Version page: P224-237 pmid: 1 publication: Cell Systems publication_identifier: issn: - 2405-4712 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 1 year: '2015' ... --- _id: '11075' abstract: - lang: eng text: Previously, we identified the nucleoporin gp210/Nup210 as a critical regulator of muscle and neuronal differentiation, but how this nucleoporin exerts its function and whether it modulates nuclear pore complex (NPC) activity remain unknown. Here, we show that gp210/Nup210 mediates muscle cell differentiation in vitro via its conserved N-terminal domain that extends into the perinuclear space. Removal of the C-terminal domain, which partially mislocalizes gp210/Nup210 away from NPCs, efficiently rescues the differentiation defect caused by the knockdown of endogenous gp210/Nup210. Unexpectedly, a gp210/Nup210 mutant lacking the NPC-targeting transmembrane and C-terminal domains is sufficient for C2C12 myoblast differentiation. We demonstrate that the endoplasmic reticulum (ER) stress-specific caspase cascade is exacerbated during Nup210 depletion and that blocking ER stress-mediated apoptosis rescues differentiation of Nup210-deficient cells. Our results suggest that the role of gp210/Nup210 in cell differentiation is mediated by its large luminal domain, which can act independently of NPC association and appears to play a pivotal role in the maintenance of nuclear envelope/ER homeostasis. article_processing_charge: No article_type: original author: - first_name: J. Sebastian full_name: Gomez-Cavazos, J. Sebastian last_name: Gomez-Cavazos - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Gomez-Cavazos JS, Hetzer M. The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis. Journal of Cell Biology. 2015;208(6):671-681. doi:10.1083/jcb.201410047 apa: Gomez-Cavazos, J. S., & Hetzer, M. (2015). The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201410047 chicago: Gomez-Cavazos, J. Sebastian, and Martin Hetzer. “The Nucleoporin Gp210/Nup210 Controls Muscle Differentiation by Regulating Nuclear Envelope/ER Homeostasis.” Journal of Cell Biology. Rockefeller University Press, 2015. https://doi.org/10.1083/jcb.201410047. ieee: J. S. Gomez-Cavazos and M. Hetzer, “The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis,” Journal of Cell Biology, vol. 208, no. 6. Rockefeller University Press, pp. 671–681, 2015. ista: Gomez-Cavazos JS, Hetzer M. 2015. The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis. Journal of Cell Biology. 208(6), 671–681. mla: Gomez-Cavazos, J. Sebastian, and Martin Hetzer. “The Nucleoporin Gp210/Nup210 Controls Muscle Differentiation by Regulating Nuclear Envelope/ER Homeostasis.” Journal of Cell Biology, vol. 208, no. 6, Rockefeller University Press, 2015, pp. 671–81, doi:10.1083/jcb.201410047. short: J.S. Gomez-Cavazos, M. Hetzer, Journal of Cell Biology 208 (2015) 671–681. date_created: 2022-04-07T07:49:10Z date_published: 2015-03-16T00:00:00Z date_updated: 2022-07-18T08:43:00Z day: '16' doi: 10.1083/jcb.201410047 extern: '1' external_id: pmid: - '25778917' intvolume: ' 208' issue: '6' keyword: - Cell Biology language: - iso: eng month: '03' oa_version: Published Version page: 671-681 pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 208 year: '2015' ... --- _id: '11076' abstract: - lang: eng text: Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation. article_processing_charge: No article_type: original author: - first_name: Arkaitz full_name: Ibarra, Arkaitz last_name: Ibarra - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Ibarra A, Hetzer M. Nuclear pore proteins and the control of genome functions. Genes & Development. 2015;29(4):337-349. doi:10.1101/gad.256495.114 apa: Ibarra, A., & Hetzer, M. (2015). Nuclear pore proteins and the control of genome functions. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.256495.114 chicago: Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control of Genome Functions.” Genes & Development. Cold Spring Harbor Laboratory, 2015. https://doi.org/10.1101/gad.256495.114. ieee: A. Ibarra and M. Hetzer, “Nuclear pore proteins and the control of genome functions,” Genes & Development, vol. 29, no. 4. Cold Spring Harbor Laboratory, pp. 337–349, 2015. ista: Ibarra A, Hetzer M. 2015. Nuclear pore proteins and the control of genome functions. Genes & Development. 29(4), 337–349. mla: Ibarra, Arkaitz, and Martin Hetzer. “Nuclear Pore Proteins and the Control of Genome Functions.” Genes & Development, vol. 29, no. 4, Cold Spring Harbor Laboratory, 2015, pp. 337–49, doi:10.1101/gad.256495.114. short: A. Ibarra, M. Hetzer, Genes & Development 29 (2015) 337–349. date_created: 2022-04-07T07:49:21Z date_published: 2015-02-01T00:00:00Z date_updated: 2022-07-18T08:43:20Z day: '01' doi: 10.1101/gad.256495.114 extern: '1' external_id: pmid: - '25691464' intvolume: ' 29' issue: '4' keyword: - Developmental Biology - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/gad.256495.114 month: '02' oa: 1 oa_version: Published Version page: 337-349 pmid: 1 publication: Genes & Development publication_identifier: eissn: - 1549-5477 issn: - 0890-9369 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: Nuclear pore proteins and the control of genome functions type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 29 year: '2015' ... --- _id: '11073' abstract: - lang: eng text: Human cancer cells bear complex chromosome rearrangements that can be potential drivers of cancer development. However, the molecular mechanisms underlying these rearrangements have been unclear. Zhang et al. use a new technique combining live-cell imaging and single-cell sequencing to demonstrate that chromosomes mis-segregated to micronuclei frequently undergo chromothripsis-like rearrangements in the subsequent cell cycle. article_processing_charge: No article_type: original author: - first_name: Emily M. full_name: Hatch, Emily M. last_name: Hatch - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Hatch EM, Hetzer M. Linking micronuclei to chromosome fragmentation. Cell. 2015;161(7):1502-1504. doi:10.1016/j.cell.2015.06.005 apa: Hatch, E. M., & Hetzer, M. (2015). Linking micronuclei to chromosome fragmentation. Cell. Elsevier. https://doi.org/10.1016/j.cell.2015.06.005 chicago: Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome Fragmentation.” Cell. Elsevier, 2015. https://doi.org/10.1016/j.cell.2015.06.005. ieee: E. M. Hatch and M. Hetzer, “Linking micronuclei to chromosome fragmentation,” Cell, vol. 161, no. 7. Elsevier, pp. 1502–1504, 2015. ista: Hatch EM, Hetzer M. 2015. Linking micronuclei to chromosome fragmentation. Cell. 161(7), 1502–1504. mla: Hatch, Emily M., and Martin Hetzer. “Linking Micronuclei to Chromosome Fragmentation.” Cell, vol. 161, no. 7, Elsevier, 2015, pp. 1502–04, doi:10.1016/j.cell.2015.06.005. short: E.M. Hatch, M. Hetzer, Cell 161 (2015) 1502–1504. date_created: 2022-04-07T07:48:49Z date_published: 2015-06-18T00:00:00Z date_updated: 2022-07-18T08:34:33Z day: '18' doi: 10.1016/j.cell.2015.06.005 extern: '1' external_id: pmid: - '26091034' intvolume: ' 161' issue: '7' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2015.06.005 month: '06' oa: 1 oa_version: Published Version page: 1502-1504 pmid: 1 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Linking micronuclei to chromosome fragmentation type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 161 year: '2015' ... --- _id: '11074' article_processing_charge: No article_type: original author: - first_name: Emily M. full_name: Hatch, Emily M. last_name: Hatch - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Hatch EM, Hetzer M. Chromothripsis. Current Biology. 2015;25(10):PR397-R399. doi:10.1016/j.cub.2015.02.033 apa: Hatch, E. M., & Hetzer, M. (2015). Chromothripsis. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2015.02.033 chicago: Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology. Elsevier, 2015. https://doi.org/10.1016/j.cub.2015.02.033. ieee: E. M. Hatch and M. Hetzer, “Chromothripsis,” Current Biology, vol. 25, no. 10. Elsevier, pp. PR397-R399, 2015. ista: Hatch EM, Hetzer M. 2015. Chromothripsis. Current Biology. 25(10), PR397-R399. mla: Hatch, Emily M., and Martin Hetzer. “Chromothripsis.” Current Biology, vol. 25, no. 10, Elsevier, 2015, pp. PR397-R399, doi:10.1016/j.cub.2015.02.033. short: E.M. Hatch, M. Hetzer, Current Biology 25 (2015) PR397-R399. date_created: 2022-04-07T07:49:00Z date_published: 2015-05-18T00:00:00Z date_updated: 2022-07-18T08:34:34Z day: '18' doi: 10.1016/j.cub.2015.02.033 extern: '1' external_id: pmid: - '25989073' intvolume: ' 25' issue: '10' keyword: - General Agricultural and Biological Sciences - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2015.02.033 month: '05' oa: 1 oa_version: Published Version page: PR397-R399 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Chromothripsis type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 25 year: '2015' ... --- _id: '11519' abstract: - lang: eng text: 'Faint Lyα emitters become increasingly rarer toward the reionization epoch (z ∼ 6–7). However, observations from a very large (∼5 deg2) Lyα narrow-band survey at z = 6.6 show that this is not the case for the most luminous emitters, capable of ionizing their own local bubbles. Here we present follow-up observations of the two most luminous Lyα candidates in the COSMOS field: “MASOSA” and “CR7.” We used X-SHOOTER, SINFONI, and FORS2 on the Very Large Telescope, and DEIMOS on Keck, to confirm both candidates beyond any doubt. We find redshifts of z = 6.541 and z = 6.604 for “MASOSA” and “CR7,” respectively. MASOSA has a strong detection in Lyα with a line width of 386 ± 30 km s−1 (FWHM) and with very high EW0 (>200 Å), but undetected in the continuum, implying very low stellar mass and a likely young, metal-poor stellar population. “CR7,” with an observed Lyα luminosity of 1043.92±0.05 erg s−1 is the most luminous Lyα emitter ever found at z > 6 and is spatially extended (∼16 kpc). “CR7” reveals a narrow Lyα line with 266 ± 15 km s−1 FWHM, being detected in the near-infrared (NIR) (rest-frame UV; β = −2.3 ± 0.1) and in IRAC/Spitzer. We detect a narrow He II 1640 Å emission line (6σ, FWHM = 130 ± 30 km s−1 ) in CR7 which can explain the clear excess seen in the J-band photometry (EW0 ∼ 80 Å). We find no other emission lines from the UV to the NIR in our X-SHOOTER spectra (He II/O III] 1663 Å > 3 and He II/C III] 1908 Å > 2.5). We conclude that CR7 is best explained by a combination of a PopIII-like population, which dominates the rest-frame UV and the nebular emission, and a more normal stellar population, which presumably dominates the mass. Hubble Space Telescope/WFC3 observations show that the light is indeed spatially separated between a very blue component, coincident with Lyα and He II emission, and two red components (∼5 kpc away), which dominate the mass. Our findings are consistent with theoretical predictions of a PopIII wave, with PopIII star formation migrating away from the original sites of star formation.' acknowledgement: We thank the anonymous reviewer for useful and constructive comments and suggestions which greatly improved the quality and clarity of our work. D.S. acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship, from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010), from FCT grant UID/FIS/04434/2013, and from LSF and LKBF. J.M. acknowledges the award of a Huygens PhD fellowship. H.R. acknowledges support from the ERC Advanced Investigator program NewClusters 321271. The authors thank Mark Dijkstra, Bhaskar Agarwal, Jarrett Johnson, Andrea Ferrara, Jarle Brinchmann, Rebecca Bowler, George Becker, Emma Curtis-Lake, Milos Milosavljevic, Raffaella Schneider, Paul Shapiro, and Erik Zackrisson for interesting, stimulating and helpful discussions. The authors are extremely grateful to ESO for the award of ESO DDT time (294.A-5018 and 294.A-5039) which allowed the spectroscopic confirmation of both sources and the detailed investigation of their nature. Observations are also based on data from W.M. Keck Observatory. The W.M. Keck Observatory is operated as a scientific partnership of Caltech, the University of California and the National Aeronautics and Space Administration. Based on observations obtained with MegaPrime/Megacam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de lUnivers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, and 179.A-2005, and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. The authors acknowledge the award of service time (SW2014b20) on the William Herschel Telescope (WHT). WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. article_processing_charge: No article_type: original author: - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Daniel full_name: Schaerer, Daniel last_name: Schaerer - first_name: Bahram full_name: Mobasher, Bahram last_name: Mobasher - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos - first_name: Shoubaneh full_name: Hemmati, Shoubaneh last_name: Hemmati citation: ama: 'Sobral D, Matthee JJ, Darvish B, et al. Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation. The Astrophysical Journal. 2015;808(2):139. doi:10.1088/0004-637X/808/2/139' apa: 'Sobral, D., Matthee, J. J., Darvish, B., Schaerer, D., Mobasher, B., Röttgering, H., … Hemmati, S. (2015). Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation. The Astrophysical Journal. IOP Publishing. https://doi.org/10.1088/0004-637X/808/2/139' chicago: 'Sobral, David, Jorryt J Matthee, Behnam Darvish, Daniel Schaerer, Bahram Mobasher, Huub Röttgering, Sérgio Santos, and Shoubaneh Hemmati. “Evidence for PopIII-like Stellar Populations in the Most Luminous Lyα Emitters at the Epoch of Reionisation: Spectroscopic Confirmation.” The Astrophysical Journal. IOP Publishing, 2015. https://doi.org/10.1088/0004-637X/808/2/139.' ieee: 'D. Sobral et al., “Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation,” The Astrophysical Journal, vol. 808, no. 2. IOP Publishing, p. 139, 2015.' ista: 'Sobral D, Matthee JJ, Darvish B, Schaerer D, Mobasher B, Röttgering H, Santos S, Hemmati S. 2015. Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation. The Astrophysical Journal. 808(2), 139.' mla: 'Sobral, David, et al. “Evidence for PopIII-like Stellar Populations in the Most Luminous Lyα Emitters at the Epoch of Reionisation: Spectroscopic Confirmation.” The Astrophysical Journal, vol. 808, no. 2, IOP Publishing, 2015, p. 139, doi:10.1088/0004-637X/808/2/139.' short: D. Sobral, J.J. Matthee, B. Darvish, D. Schaerer, B. Mobasher, H. Röttgering, S. Santos, S. Hemmati, The Astrophysical Journal 808 (2015) 139. date_created: 2022-07-07T09:00:58Z date_published: 2015-07-28T00:00:00Z date_updated: 2022-08-18T10:30:13Z day: '28' doi: 10.1088/0004-637X/808/2/139 extern: '1' external_id: arxiv: - '1504.01734' intvolume: ' 808' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - dark ages - reionization - 'first stars – early universe – galaxies: evolution' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.01734 month: '07' oa: 1 oa_version: Preprint page: '139' publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Evidence for PopIII-like stellar populations in the most luminous Lyα emitters at the epoch of reionisation: Spectroscopic confirmation' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 808 year: '2015' ... --- _id: '11580' abstract: - lang: eng text: 'We present results from the largest contiguous narrow-band survey in the near-infrared. We have used the wide-field infrared camera/Canada–France–Hawaii Telescope and the lowOH2 filter (1.187 ± 0.005 μm) to survey ≈10 deg2 of contiguous extragalactic sky in the SA22 field. A total of ∼6000 candidate emission-line galaxies are found. We use deep ugrizJK data to obtain robust photometric redshifts. We combine our data with the High-redshift(Z) Emission Line Survey (HiZELS), explore spectroscopic surveys (VVDS, VIPERS) and obtain our own spectroscopic follow-up with KMOS, FMOS and MOSFIRE to derive large samples of high-redshift emission-line selected galaxies: 3471 Hα emitters at z = 0.8, 1343 [O III] + Hβ emitters at z = 1.4 and 572 [O II] emitters at z = 2.2. We probe comoving volumes of >106 Mpc3 and find significant overdensities, including an 8.5σ (spectroscopically confirmed) overdensity of Hα emitters at z = 0.81. We derive Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4, 2.2, respectively, and present implications for future surveys such as Euclid. Our uniquely large volumes/areas allow us to subdivide the samples in thousands of randomized combinations of areas and provide a robust empirical measurement of sample/cosmic variance. We show that surveys for star-forming/emission-line galaxies at a depth similar to ours can only overcome cosmic-variance (errors <10 per cent) if they are based on volumes >5 × 105 Mpc3; errors on L* and ϕ* due to sample (cosmic) variance on surveys probing ∼104 and ∼105 Mpc3 are typically very high: ∼300 and ∼40–60 per cent, respectively.' acknowledgement: The authors wish to thank the anonymous reviewer for many helpful comments and suggestions which greatly improved the clarity and quality of this work. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship, from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010), from FCT grant PEst-OE/FIS/UI2751/2014, and from LSF and LKBF. JM acknowledges the award of a Huygens PhD fellowship. PNB is grateful for support from STFC. IRS acknowledges support from STFC, a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. BMJ acknowledges support from the ERC-StG grant EGGS-278202. The Dark Cosmology Centre is funded by the DNRF. The Dark Cosmology Centre is funded by the DNRF. JWK acknowledges support from the National Research Foundation of Korea (NRF) grant, no. 2008-0060544, funded by the Korea government (MSIP). JPS acknowledges support from STFC (ST/I001573/1). JC acknowledges support from the FCT-IF grant IF/01154/2012/CP0189/CT0010. The work was only possible due to OPTICON/FP7 and the invaluable access that it granted to the CFHT telescope. We would also like to acknowledge the excellent work done by CFHT staff in conducting the observations in service mode, and on delivering truly excellent data. We are also tremendously thankful to Kentaro Aoki for the incredible support while observing at Subaru with FMOS, and also to the Keck staff for the help with the observations with MOSFIRE. This work is based on observations obtained with WIRCam on the CFHT, OPTICON programme 2011B/029, 2012A019 and 2012B/016. Based on observations made with ESO telescopes at the La Silla Paranal Observatory under programmes IDs 60.A-9460 (data can be accessed through the ESO data archive), 087.A 0337 and 089.A-0965. Based on observations done with FMOS on Subaru under programme S14A-084, and on MOSFIRE/Keck observations under programme U066M. Part of the data on which this analysis is based are available from Sobral et al. (2013a). Dedicated to the memory of C. M. Sobral (1953-2014). article_processing_charge: No article_type: original author: - first_name: D. full_name: Sobral, D. last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: P. N. full_name: Best, P. N. last_name: Best - first_name: I. full_name: Smail, I. last_name: Smail - first_name: A. A. full_name: Khostovan, A. A. last_name: Khostovan - first_name: B. full_name: Milvang-Jensen, B. last_name: Milvang-Jensen - first_name: J.-W. full_name: Kim, J.-W. last_name: Kim - first_name: J. full_name: Stott, J. last_name: Stott - first_name: J. full_name: Calhau, J. last_name: Calhau - first_name: H. full_name: Nayyeri, H. last_name: Nayyeri - first_name: B. full_name: Mobasher, B. last_name: Mobasher citation: ama: 'Sobral D, Matthee JJ, Best PN, et al. CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 . Monthly Notices of the Royal Astronomical Society. 2015;451(3):2303-2323. doi:10.1093/mnras/stv1076' apa: 'Sobral, D., Matthee, J. J., Best, P. N., Smail, I., Khostovan, A. A., Milvang-Jensen, B., … Mobasher, B. (2015). CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 . Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv1076' chicago: 'Sobral, D., Jorryt J Matthee, P. N. Best, I. Smail, A. A. Khostovan, B. Milvang-Jensen, J.-W. Kim, et al. “CF-HiZELS, an ∼10 Deg2 Emission-Line Survey with Spectroscopic Follow-up: Hα, [O III] + Hβ and [O II] Luminosity Functions at z = 0.8, 1.4 and 2.2 .” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv1076.' ieee: 'D. Sobral et al., “CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 ,” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 3. Oxford University Press, pp. 2303–2323, 2015.' ista: 'Sobral D, Matthee JJ, Best PN, Smail I, Khostovan AA, Milvang-Jensen B, Kim J-W, Stott J, Calhau J, Nayyeri H, Mobasher B. 2015. CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 . Monthly Notices of the Royal Astronomical Society. 451(3), 2303–2323.' mla: 'Sobral, D., et al. “CF-HiZELS, an ∼10 Deg2 Emission-Line Survey with Spectroscopic Follow-up: Hα, [O III] + Hβ and [O II] Luminosity Functions at z = 0.8, 1.4 and 2.2 .” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 3, Oxford University Press, 2015, pp. 2303–23, doi:10.1093/mnras/stv1076.' short: D. Sobral, J.J. Matthee, P.N. Best, I. Smail, A.A. Khostovan, B. Milvang-Jensen, J.-W. Kim, J. Stott, J. Calhau, H. Nayyeri, B. Mobasher, Monthly Notices of the Royal Astronomical Society 451 (2015) 2303–2323. date_created: 2022-07-14T09:02:22Z date_published: 2015-08-11T00:00:00Z date_updated: 2022-08-19T08:23:18Z day: '11' doi: 10.1093/mnras/stv1076 extern: '1' external_id: arxiv: - '1502.06602' intvolume: ' 451' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: formation' - 'galaxies: luminosity function' - mass function - 'cosmology: observations' - early Universe - large-scale structure of Universe language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1502.06602 month: '08' oa: 1 oa_version: Preprint page: 2303-2323 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'CF-HiZELS, an ∼10 deg2 emission-line survey with spectroscopic follow-up: Hα, [O III] + Hβ and [O II] luminosity functions at z = 0.8, 1.4 and 2.2 ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 451 year: '2015' ... --- _id: '11581' abstract: - lang: eng text: Using wide-field narrow-band surveys, we provide a new measurement of the z = 6.6 Lymanα emitter (LAE) luminosity function (LF), which constraints the bright end for the first time. We use a combination of archival narrow-band NB921 data in UDS and new NB921 measurements in SA22 and COSMOS/UltraVISTA, all observed with the Subaru telescope, with a total area of ∼5 deg2. We exclude lower redshift interlopers by using broad-band optical and near-infrared photometry and also exclude three supernovae with data split over multiple epochs. Combining the UDS and COSMOS samples, we find no evolution of the bright end of the Lyα LF between z = 5.7 and 6.6, which is supported by spectroscopic follow-up, and conclude that sources with Himiko-like luminosity are not as rare as previously thought, with number densities of ∼1.5 × 10−5 Mpc−3. Combined with our wide-field SA22 measurements, our results indicate a non-Schechter-like bright end of the LF at z = 6.6 and a different evolution of observed faint and bright LAEs, overcoming cosmic variance. This differential evolution is also seen in the spectroscopic follow-up of UV-selected galaxies and is now also confirmed for LAEs, and we argue that it may be an effect of reionization. Using a toy model, we show that such differential evolution of the LF is expected, since brighter sources are able to ionize their surroundings earlier, such that Lyα photons are able to escape. Our targets are excellent candidates for detailed follow-up studies and provide the possibility to give a unique view on the earliest stages in the formation of galaxies and reionization process. acknowledgement: "We thank the anonymous referee for the comments and suggestions which have improved the quality of this work. We thank Masami Ouchi for his useful comments on an earlier version of this paper. JM acknowledges the support of a Huygens PhD fellowship from Leiden University and is thankful for the hospitality of the Center for Astronomy and Astrophysics of the University of Lisbon where part of this research has been done. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship, from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEstOE/FIS/UI2751/2014. HR acknowledges support from the ERC Advanced Investigator programme NewClusters 321271. We acknowledge the award of ESO DDT time (294.A-5018) for providing the possibility of a timely publication of this work.\r\nBased on observations with the Subaru Telescope (Programme IDs: our observations: S14A-086; archival: S05B-027, S06A-025, S06B-010, S07A-013, S07B-008, S08B-008 and S09A-017) and the W.M. Keck Observatory. The Subaru telescope is operated by the National Astronomical Observatory of Japan. The W.M. Keck Observatory is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. Based on observations obtained with MegaPrime/Megacam, a joint project of CFHT and CEA/IRFU, at the Canada–France-Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the CFHT Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme ID 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium.\r\nIn addition to the CFHT-LS and COSMOS-UltraVISTA surveys, we are grateful for the excellent data sets from the UKIRT-DXS, SXDF and S-COSMOS survey teams, without these legacy surveys, this research would have been impossible. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP and SCAMP and the indispensable TOPCAT analysis tool (Taylor 2013)" article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Bahram full_name: Mobasher, Bahram last_name: Mobasher citation: ama: 'Matthee JJ, Sobral D, Santos S, Röttgering H, Darvish B, Mobasher B. Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era. Monthly Notices of the Royal Astronomical Society. 2015;451(1):400-417. doi:10.1093/mnras/stv947' apa: 'Matthee, J. J., Sobral, D., Santos, S., Röttgering, H., Darvish, B., & Mobasher, B. (2015). Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv947' chicago: 'Matthee, Jorryt J, David Sobral, Sérgio Santos, Huub Röttgering, Behnam Darvish, and Bahram Mobasher. “Identification of the Brightest Lyα Emitters at z = 6.6: Implications for the Evolution of the Luminosity Function in the Reionization Era.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv947.' ieee: 'J. J. Matthee, D. Sobral, S. Santos, H. Röttgering, B. Darvish, and B. Mobasher, “Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era,” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 1. Oxford University Press, pp. 400–417, 2015.' ista: 'Matthee JJ, Sobral D, Santos S, Röttgering H, Darvish B, Mobasher B. 2015. Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era. Monthly Notices of the Royal Astronomical Society. 451(1), 400–417.' mla: 'Matthee, Jorryt J., et al. “Identification of the Brightest Lyα Emitters at z = 6.6: Implications for the Evolution of the Luminosity Function in the Reionization Era.” Monthly Notices of the Royal Astronomical Society, vol. 451, no. 1, Oxford University Press, 2015, pp. 400–17, doi:10.1093/mnras/stv947.' short: J.J. Matthee, D. Sobral, S. Santos, H. Röttgering, B. Darvish, B. Mobasher, Monthly Notices of the Royal Astronomical Society 451 (2015) 400–417. date_created: 2022-07-14T11:57:03Z date_published: 2015-07-21T00:00:00Z date_updated: 2022-08-19T08:25:25Z day: '21' doi: 10.1093/mnras/stv947 extern: '1' external_id: arxiv: - '1502.07355' intvolume: ' 451' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1502.07355 month: '07' oa: 1 oa_version: Preprint page: 400-417 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Identification of the brightest Lyα emitters at z = 6.6: implications for the evolution of the luminosity function in the reionization era' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 451 year: '2015' ... --- _id: '11579' abstract: - lang: eng text: CR7 is the brightest z = 6.6 Ly α emitter (LAE) known to date, and spectroscopic follow-up by Sobral et al. suggests that CR7 might host Population (Pop) III stars. We examine this interpretation using cosmological hydrodynamical simulations. Several simulated galaxies show the same ‘Pop III wave’ pattern observed in CR7. However, to reproduce the extreme CR7 Ly α/He II1640 line luminosities (⁠Lα/HeII⁠) a top-heavy initial mass function and a massive ( ≳ 107 M⊙) Pop III burst with age ≲ 2 Myr are required. Assuming that the observed properties of Ly α and He II emission are typical for Pop III, we predict that in the COSMOS/UDS/SA22 fields, 14 out of the 30 LAEs at z = 6.6 with Lα > 1043.3 erg s−1 should also host Pop III stars producing an observable LHeII≳1042.7ergs−1⁠. As an alternate explanation, we explore the possibility that CR7 is instead powered by accretion on to a direct collapse black hole. Our model predicts Lα, LHeII⁠, and X-ray luminosities that are in agreement with the observations. In any case, the observed properties of CR7 indicate that this galaxy is most likely powered by sources formed from pristine gas. We propose that further X-ray observations can distinguish between the two above scenarios. acknowledgement: SS acknowledges support from the Netherlands Organization for Scientific research (NWO), VENI grant 639.041.233. RS acknowledges support from the European Research Council under the European Union (FP/2007-2013)/ERC grant agreement no. 306476. DS acknowledges (i) financial support from the NWO through a Veni fellowship and (ii) funding from FCT through a FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010) and from FCT grant PEstOE/FIS/UI2751/2014. article_processing_charge: No article_type: original author: - first_name: A. full_name: Pallottini, A. last_name: Pallottini - first_name: A. full_name: Ferrara, A. last_name: Ferrara - first_name: F. full_name: Pacucci, F. last_name: Pacucci - first_name: S. full_name: Gallerani, S. last_name: Gallerani - first_name: S. full_name: Salvadori, S. last_name: Salvadori - first_name: R. full_name: Schneider, R. last_name: Schneider - first_name: D. full_name: Schaerer, D. last_name: Schaerer - first_name: D. full_name: Sobral, D. last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X citation: ama: 'Pallottini A, Ferrara A, Pacucci F, et al. The brightest Lyα emitter: Pop III or black hole? Monthly Notices of the Royal Astronomical Society. 2015;453(3):2465-2470. doi:10.1093/mnras/stv1795' apa: 'Pallottini, A., Ferrara, A., Pacucci, F., Gallerani, S., Salvadori, S., Schneider, R., … Matthee, J. J. (2015). The brightest Lyα emitter: Pop III or black hole? Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stv1795' chicago: 'Pallottini, A., A. Ferrara, F. Pacucci, S. Gallerani, S. Salvadori, R. Schneider, D. Schaerer, D. Sobral, and Jorryt J Matthee. “The Brightest Lyα Emitter: Pop III or Black Hole?” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2015. https://doi.org/10.1093/mnras/stv1795.' ieee: 'A. Pallottini et al., “The brightest Lyα emitter: Pop III or black hole?,” Monthly Notices of the Royal Astronomical Society, vol. 453, no. 3. Oxford University Press, pp. 2465–2470, 2015.' ista: 'Pallottini A, Ferrara A, Pacucci F, Gallerani S, Salvadori S, Schneider R, Schaerer D, Sobral D, Matthee JJ. 2015. The brightest Lyα emitter: Pop III or black hole? Monthly Notices of the Royal Astronomical Society. 453(3), 2465–2470.' mla: 'Pallottini, A., et al. “The Brightest Lyα Emitter: Pop III or Black Hole?” Monthly Notices of the Royal Astronomical Society, vol. 453, no. 3, Oxford University Press, 2015, pp. 2465–70, doi:10.1093/mnras/stv1795.' short: A. Pallottini, A. Ferrara, F. Pacucci, S. Gallerani, S. Salvadori, R. Schneider, D. Schaerer, D. Sobral, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 453 (2015) 2465–2470. date_created: 2022-07-14T08:58:36Z date_published: 2015-11-01T00:00:00Z date_updated: 2022-08-19T08:19:23Z day: '01' doi: 10.1093/mnras/stv1795 extern: '1' external_id: arxiv: - '1506.07173' intvolume: ' 453' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - black hole physics - 'stars: Population III' - 'galaxies: high-redshift' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1506.07173 month: '11' oa: 1 oa_version: Preprint page: 2465-2470 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The brightest Lyα emitter: Pop III or black hole?' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 453 year: '2015' ... --- _id: '11668' abstract: - lang: eng text: "We study multiple keyword sponsored search auctions with budgets. Each keyword has multiple ad slots with a click-through rate. The bidders have additive valuations, which are linear in the click-through rates, and budgets, which are restricting their overall payments. Additionally, the number of slots per keyword assigned to a bidder is bounded.\r\n\r\nWe show the following results: (1) We give the first mechanism for multiple keywords, where click-through rates differ among slots. Our mechanism is incentive compatible in expectation, individually rational in expectation, and Pareto optimal. (2) We study the combinatorial setting, where each bidder is only interested in a subset of the keywords. We give an incentive compatible, individually rational, Pareto-optimal, and deterministic mechanism for identical click-through rates. (3) We give an impossibility result for incentive compatible, individually rational, Pareto-optimal, and deterministic mechanisms for bidders with diminishing marginal valuations." article_number: '2' article_processing_charge: No article_type: original author: - first_name: Riccardo full_name: Colini-Baldeschi, Riccardo last_name: Colini-Baldeschi - first_name: Stefano full_name: Leonardi, Stefano last_name: Leonardi - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: Colini-Baldeschi R, Leonardi S, Henzinger MH, Starnberger M. On multiple keyword sponsored search auctions with budgets. ACM Transactions on Economics and Computation. 2015;4(1). doi:10.1145/2818357 apa: Colini-Baldeschi, R., Leonardi, S., Henzinger, M. H., & Starnberger, M. (2015). On multiple keyword sponsored search auctions with budgets. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/2818357 chicago: Colini-Baldeschi, Riccardo, Stefano Leonardi, Monika H Henzinger, and Martin Starnberger. “On Multiple Keyword Sponsored Search Auctions with Budgets.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2015. https://doi.org/10.1145/2818357. ieee: R. Colini-Baldeschi, S. Leonardi, M. H. Henzinger, and M. Starnberger, “On multiple keyword sponsored search auctions with budgets,” ACM Transactions on Economics and Computation, vol. 4, no. 1. Association for Computing Machinery, 2015. ista: Colini-Baldeschi R, Leonardi S, Henzinger MH, Starnberger M. 2015. On multiple keyword sponsored search auctions with budgets. ACM Transactions on Economics and Computation. 4(1), 2. mla: Colini-Baldeschi, Riccardo, et al. “On Multiple Keyword Sponsored Search Auctions with Budgets.” ACM Transactions on Economics and Computation, vol. 4, no. 1, 2, Association for Computing Machinery, 2015, doi:10.1145/2818357. short: R. Colini-Baldeschi, S. Leonardi, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics and Computation 4 (2015). date_created: 2022-07-27T11:54:56Z date_published: 2015-12-05T00:00:00Z date_updated: 2023-02-09T10:03:35Z day: '05' doi: 10.1145/2818357 extern: '1' intvolume: ' 4' issue: '1' keyword: - Algorithms - Economics - Clinching ascending auction - auctions with budgets - Sponsored search auctions language: - iso: eng main_file_link: - open_access: '1' url: http://eprints.cs.univie.ac.at/3510/ month: '12' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Economics and Computation publication_identifier: eissn: - 2167-8383 issn: - 2167-8375 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: On multiple keyword sponsored search auctions with budgets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '11669' abstract: - lang: eng text: We study individual rational, Pareto-optimal, and incentive compatible mechanisms for auctions with heterogeneous items and budget limits. We consider settings with multiunit demand and additive valuations. For single-dimensional valuations we prove a positive result for randomized mechanisms, and a negative result for deterministic mechanisms. While the positive result allows for private budgets, the negative result is for public budgets. For multidimensional valuations and public budgets we prove an impossibility result that applies to deterministic and randomized mechanisms. Taken together this shows the power of randomization in certain settings with heterogeneous items, but it also shows its limitations. article_number: '4' article_processing_charge: No article_type: original author: - first_name: Paul full_name: Dütting, Paul last_name: Dütting - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: Dütting P, Henzinger MH, Starnberger M. Auctions for heterogeneous items and budget limits. ACM Transactions on Economics and Computation. 2015;4(1). doi:10.1145/2818351 apa: Dütting, P., Henzinger, M. H., & Starnberger, M. (2015). Auctions for heterogeneous items and budget limits. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/2818351 chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Auctions for Heterogeneous Items and Budget Limits.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2015. https://doi.org/10.1145/2818351. ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Auctions for heterogeneous items and budget limits,” ACM Transactions on Economics and Computation, vol. 4, no. 1. Association for Computing Machinery, 2015. ista: Dütting P, Henzinger MH, Starnberger M. 2015. Auctions for heterogeneous items and budget limits. ACM Transactions on Economics and Computation. 4(1), 4. mla: Dütting, Paul, et al. “Auctions for Heterogeneous Items and Budget Limits.” ACM Transactions on Economics and Computation, vol. 4, no. 1, 4, Association for Computing Machinery, 2015, doi:10.1145/2818351. short: P. Dütting, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics and Computation 4 (2015). date_created: 2022-07-27T12:09:15Z date_published: 2015-12-05T00:00:00Z date_updated: 2022-09-09T12:08:37Z day: '05' doi: 10.1145/2818351 extern: '1' external_id: arxiv: - '1209.6448' intvolume: ' 4' issue: '1' keyword: - Algorithmic game theory - auction theory - Clinching auction - Pareto optimality - Budget limits language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1209.6448 month: '12' oa: 1 oa_version: Preprint publication: ACM Transactions on Economics and Computation publication_identifier: eissn: - 2167-8383 issn: - 2167-8375 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Auctions for heterogeneous items and budget limits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '11670' abstract: - lang: eng text: Auctions are widely used on the Web. Applications range from sponsored search to platforms such as eBay. In these and in many other applications the auctions in use are single-/multi-item auctions with unit demand. The main drawback of standard mechanisms for this type of auctions, such as VCG and GSP, is the limited expressiveness that they offer to the bidders. The General Auction Mechanism (GAM) of Aggarwal et al. [2009] takes a first step toward addressing the problem of limited expressiveness by computing a bidder optimal, envy-free outcome for linear utility functions with identical slopes and a single discontinuity per bidder-item pair. We show that in many practical situations this does not suffice to adequately model the preferences of the bidders, and we overcome this problem by presenting the first mechanism for piecewise linear utility functions with nonidentical slopes and multiple discontinuities. Our mechanism runs in polynomial time. Like GAM it is incentive compatible for inputs that fulfill a certain nondegeneracy assumption, but our requirement is more general than the requirement of GAM. For discontinuous utility functions that are nondegenerate as well as for continuous utility functions the outcome of our mechanism is a competitive equilibrium. We also show how our mechanism can be used to compute approximately bidder optimal, envy-free outcomes for a general class of continuous utility functions via piecewise linear approximation. Finally, we prove hardness results for even more expressive settings. acknowledgement: We would like to thank Veronika Loitzenbauer and the anonymous referees for their valuable feedback. article_number: '1' article_processing_charge: No article_type: original author: - first_name: Paul full_name: Dütting, Paul last_name: Dütting - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Ingmar full_name: Weber, Ingmar last_name: Weber citation: ama: Dütting P, Henzinger MH, Weber I. An expressive mechanism for auctions on the web. ACM Transactions on Economics and Computation. 2015;4(1). doi:10.1145/2716312 apa: Dütting, P., Henzinger, M. H., & Weber, I. (2015). An expressive mechanism for auctions on the web. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/2716312 chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “An Expressive Mechanism for Auctions on the Web.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2015. https://doi.org/10.1145/2716312. ieee: P. Dütting, M. H. Henzinger, and I. Weber, “An expressive mechanism for auctions on the web,” ACM Transactions on Economics and Computation, vol. 4, no. 1. Association for Computing Machinery, 2015. ista: Dütting P, Henzinger MH, Weber I. 2015. An expressive mechanism for auctions on the web. ACM Transactions on Economics and Computation. 4(1), 1. mla: Dütting, Paul, et al. “An Expressive Mechanism for Auctions on the Web.” ACM Transactions on Economics and Computation, vol. 4, no. 1, 1, Association for Computing Machinery, 2015, doi:10.1145/2716312. short: P. Dütting, M.H. Henzinger, I. Weber, ACM Transactions on Economics and Computation 4 (2015). date_created: 2022-07-27T12:43:18Z date_published: 2015-12-02T00:00:00Z date_updated: 2023-02-09T10:08:41Z day: '02' doi: 10.1145/2716312 extern: '1' intvolume: ' 4' issue: '1' keyword: - Computational Mathematics - Marketing - Economics and Econometrics - Statistics and Probability - Computer Science (miscellaneous) language: - iso: eng month: '12' oa_version: None publication: ACM Transactions on Economics and Computation publication_identifier: eissn: - 2167-8383 issn: - 2167-8375 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: An expressive mechanism for auctions on the web type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '11774' abstract: - lang: eng text: "Combinatorial auctions (CA) are a well-studied area in algorithmic mechanism design. However, contrary to the standard model, empirical studies suggest that a bidder’s valuation often does not depend solely on the goods assigned to him. For instance, in adwords auctions an advertiser might not want his ads to be displayed next to his competitors’ ads. In this paper, we propose and analyze several natural graph-theoretic models that incorporate such negative externalities, in which bidders form a directed conflict graph with maximum out-degree Δ. We design algorithms and truthful mechanisms for social welfare maximization that attain approximation ratios depending on Δ.\r\n\r\nFor CA, our results are twofold: (1) A lottery that eliminates conflicts by discarding bidders/items independent of the bids. It allows to apply any truthful \U0001D6FC-approximation mechanism for conflict-free valuations and yields an \U0001D4AA(\U0001D6FCΔ)-approximation mechanism. (2) For fractionally sub-additive valuations, we design a rounding algorithm via a novel combination of a semi-definite program and a linear program, resulting in a cone program; the approximation ratio is \U0001D4AA((ΔloglogΔ)/logΔ). The ratios are almost optimal given existing hardness results.\r\n\r\nFor adwords auctions, we present several algorithms for the most relevant scenario when the number of items is small. In particular, we design a truthful mechanism with approximation ratio \U0001D45C(Δ) when the number of items is only logarithmic in the number of bidders." alternative_title: - LNCS article_processing_charge: No author: - first_name: Yun Kuen full_name: Cheung, Yun Kuen last_name: Cheung - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Hoefer, Martin last_name: Hoefer - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: 'Cheung YK, Henzinger MH, Hoefer M, Starnberger M. Combinatorial auctions with conflict-based externalities. In: 11th International Conference on Web and Internet Economics. Vol 9470. Springer Nature; 2015:230–243. doi:10.1007/978-3-662-48995-6_17' apa: 'Cheung, Y. K., Henzinger, M. H., Hoefer, M., & Starnberger, M. (2015). Combinatorial auctions with conflict-based externalities. In 11th International Conference on Web and Internet Economics (Vol. 9470, pp. 230–243). Amsterdam, Netherlands: Springer Nature. https://doi.org/10.1007/978-3-662-48995-6_17' chicago: Cheung, Yun Kuen, Monika H Henzinger, Martin Hoefer, and Martin Starnberger. “Combinatorial Auctions with Conflict-Based Externalities.” In 11th International Conference on Web and Internet Economics, 9470:230–243. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48995-6_17. ieee: Y. K. Cheung, M. H. Henzinger, M. Hoefer, and M. Starnberger, “Combinatorial auctions with conflict-based externalities,” in 11th International Conference on Web and Internet Economics, Amsterdam, Netherlands, 2015, vol. 9470, pp. 230–243. ista: 'Cheung YK, Henzinger MH, Hoefer M, Starnberger M. 2015. Combinatorial auctions with conflict-based externalities. 11th International Conference on Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 9470, 230–243.' mla: Cheung, Yun Kuen, et al. “Combinatorial Auctions with Conflict-Based Externalities.” 11th International Conference on Web and Internet Economics, vol. 9470, Springer Nature, 2015, pp. 230–243, doi:10.1007/978-3-662-48995-6_17. short: Y.K. Cheung, M.H. Henzinger, M. Hoefer, M. Starnberger, in:, 11th International Conference on Web and Internet Economics, Springer Nature, 2015, pp. 230–243. conference: end_date: 2015-12-12 location: Amsterdam, Netherlands name: 'WINE: International Conference on Web and Internet Economics' start_date: 2015-12-09 date_created: 2022-08-08T13:54:32Z date_published: 2015-12-09T00:00:00Z date_updated: 2023-02-10T09:08:30Z day: '09' doi: 10.1007/978-3-662-48995-6_17 extern: '1' external_id: arxiv: - '1509.09147' intvolume: ' 9470' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1509.09147 month: '12' oa: 1 oa_version: Preprint page: 230–243 publication: 11th International Conference on Web and Internet Economics publication_identifier: eisbn: - '9783662489956' isbn: - '9783662489949' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Combinatorial auctions with conflict-based externalities type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9470 year: '2015' ... --- _id: '11773' abstract: - lang: eng text: "Ad exchanges are an emerging platform for trading advertisement slots on the web with billions of dollars revenue per year. Every time a user visits a web page, the publisher of that web page can ask an ad exchange to auction off the ad slots on this page to determine which advertisements are shown at which price. Due to the high volume of traffic, ad networks typically act as mediators for individual advertisers at ad exchanges. If multiple advertisers in an ad network are interested in the ad slots of the same auction, the ad network might use a “local” auction to resell the obtained ad slots among its advertisers.\r\n\r\nIn this work we want to deepen the theoretical understanding of these new markets by analyzing them from the viewpoint of combinatorial auctions. Prior work studied mostly single-item auctions, while we allow the advertisers to express richer preferences over multiple items. We develop a game-theoretic model for the entanglement of the central auction at the ad exchange with the local auctions at the ad networks. We consider the incentives of all three involved parties and suggest a three-party competitive equilibrium, an extension of the Walrasian equilibrium that ensures envy-freeness for all participants. We show the existence of a three-party competitive equilibrium and a polynomial-time algorithm to find one for gross-substitute bidder valuations." alternative_title: - LNCS article_processing_charge: No author: - first_name: Oren full_name: Ben-Zwi, Oren last_name: Ben-Zwi - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: 'Ben-Zwi O, Henzinger MH, Loitzenbauer V. Ad exchange: Envy-free auctions with mediators. In: 11th International Conference on Web and Internet Economics. Vol 9470. Springer Nature; 2015:104–117. doi:10.1007/978-3-662-48995-6_8' apa: 'Ben-Zwi, O., Henzinger, M. H., & Loitzenbauer, V. (2015). Ad exchange: Envy-free auctions with mediators. In 11th International Conference on Web and Internet Economics (Vol. 9470, pp. 104–117). Amsterdam, Netherlands: Springer Nature. https://doi.org/10.1007/978-3-662-48995-6_8' chicago: 'Ben-Zwi, Oren, Monika H Henzinger, and Veronika Loitzenbauer. “Ad Exchange: Envy-Free Auctions with Mediators.” In 11th International Conference on Web and Internet Economics, 9470:104–117. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48995-6_8.' ieee: 'O. Ben-Zwi, M. H. Henzinger, and V. Loitzenbauer, “Ad exchange: Envy-free auctions with mediators,” in 11th International Conference on Web and Internet Economics, Amsterdam, Netherlands, 2015, vol. 9470, pp. 104–117.' ista: 'Ben-Zwi O, Henzinger MH, Loitzenbauer V. 2015. Ad exchange: Envy-free auctions with mediators. 11th International Conference on Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 9470, 104–117.' mla: 'Ben-Zwi, Oren, et al. “Ad Exchange: Envy-Free Auctions with Mediators.” 11th International Conference on Web and Internet Economics, vol. 9470, Springer Nature, 2015, pp. 104–117, doi:10.1007/978-3-662-48995-6_8.' short: O. Ben-Zwi, M.H. Henzinger, V. Loitzenbauer, in:, 11th International Conference on Web and Internet Economics, Springer Nature, 2015, pp. 104–117. conference: end_date: 2015-09-12 location: Amsterdam, Netherlands name: 'WINE: International Conference on Web and Internet Economics' start_date: 2015-09-09 date_created: 2022-08-08T13:33:56Z date_published: 2015-12-09T00:00:00Z date_updated: 2023-02-10T09:06:23Z day: '09' doi: 10.1007/978-3-662-48995-6_8 extern: '1' external_id: arxiv: - '1604.05562' intvolume: ' 9470' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1604.05562 month: '12' oa: 1 oa_version: Preprint page: 104–117 publication: 11th International Conference on Web and Internet Economics publication_identifier: eisbn: - '9783662489956' isbn: - '9783662489949' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Ad exchange: Envy-free auctions with mediators' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9470 year: '2015' ... --- _id: '11785' abstract: - lang: eng text: "Recently we presented the first algorithm for maintaining the set of nodes reachable from a source node in a directed graph that is modified by edge deletions with \U0001D45C(\U0001D45A\U0001D45B) total update time, where \U0001D45A is the number of edges and \U0001D45B is the number of nodes in the graph [Henzinger et al. STOC 2014]. The algorithm is a combination of several different algorithms, each for a different \U0001D45A vs. \U0001D45B trade-off. For the case of \U0001D45A=Θ(\U0001D45B1.5) the running time is \U0001D442(\U0001D45B2.47), just barely below \U0001D45A\U0001D45B=Θ(\U0001D45B2.5). In this paper we simplify the previous algorithm using new algorithmic ideas and achieve an improved running time of \U0001D442̃ (min(\U0001D45A7/6\U0001D45B2/3,\U0001D45A3/4\U0001D45B5/4+\U0001D45C(1),\U0001D45A2/3\U0001D45B4/3+\U0001D45C(1)+\U0001D45A3/7\U0001D45B12/7+\U0001D45C(1))). This gives, e.g., \U0001D442(\U0001D45B2.36) for the notorious case \U0001D45A=Θ(\U0001D45B1.5). We obtain the same upper bounds for the problem of maintaining the strongly connected components of a directed graph undergoing edge deletions. Our algorithms are correct with high probabililty against an oblivious adversary." alternative_title: - LNCS article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D. Improved algorithms for decremental single-source reachability on directed graphs. In: 42nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:725-736. doi:10.1007/978-3-662-47672-7_59' apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2015). Improved algorithms for decremental single-source reachability on directed graphs. In 42nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 725–736). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_59' chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Improved Algorithms for Decremental Single-Source Reachability on Directed Graphs.” In 42nd International Colloquium on Automata, Languages and Programming, 9134:725–36. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_59. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Improved algorithms for decremental single-source reachability on directed graphs,” in 42nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 725–736. ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2015. Improved algorithms for decremental single-source reachability on directed graphs. 42nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 725–736.' mla: Henzinger, Monika H., et al. “Improved Algorithms for Decremental Single-Source Reachability on Directed Graphs.” 42nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 725–36, doi:10.1007/978-3-662-47672-7_59. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 725–736. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2015-07-06 date_created: 2022-08-11T08:51:32Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-10T09:10:26Z day: '01' doi: 10.1007/978-3-662-47672-7_59 extern: '1' external_id: arxiv: - '1612.03856' intvolume: ' 9134' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.03856 month: '01' oa: 1 oa_version: Preprint page: 725 - 736 publication: 42nd International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - '9783662476710' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Improved algorithms for decremental single-source reachability on directed graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9134 year: '2015' ... --- _id: '11787' abstract: - lang: eng text: "We present faster algorithms for computing the 2-edge and 2-vertex strongly connected components of a directed graph. While in undirected graphs the 2-edge and 2-vertex connected components can be found in linear time, in directed graphs with m edges and n vertices only rather simple O(m n)-time algorithms were known. We use a hierarchical sparsification technique to obtain algorithms that run in time \U0001D442(\U0001D45B2). For 2-edge strongly connected components our algorithm gives the first running time improvement in 20 years. Additionally we present an \U0001D442(\U0001D45A2/log\U0001D45B)-time algorithm for 2-edge strongly connected components, and thus improve over the O(m n) running time also when \U0001D45A=\U0001D442(\U0001D45B). Our approach extends to k-edge and k-vertex strongly connected components for any constant k with a running time of \U0001D442(\U0001D45B2log\U0001D45B) for k-edge-connectivity and \U0001D442(\U0001D45B3) for k-vertex-connectivity." alternative_title: - LNCS article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: 'Henzinger MH, Krinninger S, Loitzenbauer V. Finding 2-edge and 2-vertex strongly connected components in quadratic time. In: 2nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:713-724. doi:10.1007/978-3-662-47672-7_58' apa: 'Henzinger, M. H., Krinninger, S., & Loitzenbauer, V. (2015). Finding 2-edge and 2-vertex strongly connected components in quadratic time. In 2nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 713–724). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_58' chicago: Henzinger, Monika H, Sebastian Krinninger, and Veronika Loitzenbauer. “Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time.” In 2nd International Colloquium on Automata, Languages and Programming, 9134:713–24. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_58. ieee: M. H. Henzinger, S. Krinninger, and V. Loitzenbauer, “Finding 2-edge and 2-vertex strongly connected components in quadratic time,” in 2nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 713–724. ista: 'Henzinger MH, Krinninger S, Loitzenbauer V. 2015. Finding 2-edge and 2-vertex strongly connected components in quadratic time. 2nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 713–724.' mla: Henzinger, Monika H., et al. “Finding 2-Edge and 2-Vertex Strongly Connected Components in Quadratic Time.” 2nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 713–24, doi:10.1007/978-3-662-47672-7_58. short: M.H. Henzinger, S. Krinninger, V. Loitzenbauer, in:, 2nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 713–724. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2015-07-06 date_created: 2022-08-11T09:38:34Z date_published: 2015-07-06T00:00:00Z date_updated: 2023-02-10T09:21:47Z day: '06' doi: 10.1007/978-3-662-47672-7_58 extern: '1' external_id: arxiv: - '1412.6466' intvolume: ' 9134' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.6466 month: '07' oa: 1 oa_version: Preprint page: 713 - 724 publication: 2nd International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - '9783662476710' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Finding 2-edge and 2-vertex strongly connected components in quadratic time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9134 year: '2015' ... --- _id: '11788' abstract: - lang: eng text: "Ad exchanges are becoming an increasingly popular way to sell advertisement slots on the internet. An ad exchange is basically a spot market for ad impressions. A publisher who has already signed contracts reserving advertisement impressions on his pages can choose between assigning a new ad impression for a new page view to a contracted advertiser or to sell it at an ad exchange. This leads to an online revenue maximization problem for the publisher. Given a new impression to sell decide whether (a) to assign it to a contracted advertiser and if so to which one or (b) to sell it at the ad exchange and if so at which reserve price. We make no assumptions about the distribution of the advertiser valuations that participate in the ad exchange and show that there exists a simple primal-dual based online algorithm, whose lower bound for the revenue converges to \U0001D445\U0001D434\U0001D437\U0001D44B+\U0001D445\U0001D434(1−1/\U0001D452), where \U0001D445\U0001D434\U0001D437\U0001D44B is the revenue that the optimum algorithm achieves from the ad exchange and \U0001D445\U0001D434 is the revenue that the optimum algorithm achieves from the contracted advertisers." alternative_title: - LNCS article_processing_charge: No author: - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Dvořák W, Henzinger MH. Online ad assignment with an ad exchange. In: 12th International Workshop of Approximation and Online Algorithms. Vol 8952. Springer Nature; 2015:156–167. doi:10.1007/978-3-319-18263-6_14' apa: 'Dvořák, W., & Henzinger, M. H. (2015). Online ad assignment with an ad exchange. In 12th International Workshop of Approximation and Online Algorithms (Vol. 8952, pp. 156–167). Wroclaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-319-18263-6_14' chicago: Dvořák, Wolfgang, and Monika H Henzinger. “Online Ad Assignment with an Ad Exchange.” In 12th International Workshop of Approximation and Online Algorithms, 8952:156–167. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-18263-6_14. ieee: W. Dvořák and M. H. Henzinger, “Online ad assignment with an ad exchange,” in 12th International Workshop of Approximation and Online Algorithms, Wroclaw, Poland, 2015, vol. 8952, pp. 156–167. ista: 'Dvořák W, Henzinger MH. 2015. Online ad assignment with an ad exchange. 12th International Workshop of Approximation and Online Algorithms. WAOA: International Workshop on Approximation and Online Algorithms, LNCS, vol. 8952, 156–167.' mla: Dvořák, Wolfgang, and Monika H. Henzinger. “Online Ad Assignment with an Ad Exchange.” 12th International Workshop of Approximation and Online Algorithms, vol. 8952, Springer Nature, 2015, pp. 156–167, doi:10.1007/978-3-319-18263-6_14. short: W. Dvořák, M.H. Henzinger, in:, 12th International Workshop of Approximation and Online Algorithms, Springer Nature, 2015, pp. 156–167. conference: end_date: 2014-09-12 location: Wroclaw, Poland name: 'WAOA: International Workshop on Approximation and Online Algorithms' start_date: 2014-09-11 date_created: 2022-08-11T09:43:32Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-10T09:26:06Z day: '01' doi: 10.1007/978-3-319-18263-6_14 extern: '1' external_id: arxiv: - '1604.05603' intvolume: ' 8952' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.05603 month: '01' oa: 1 oa_version: Preprint page: 156–167 publication: 12th International Workshop of Approximation and Online Algorithms publication_identifier: issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Online ad assignment with an ad exchange type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8952 year: '2015' ... --- _id: '11786' abstract: - lang: eng text: "In this paper, we develop a dynamic version of the primal-dual method for optimization problems, and apply it to obtain the following results. (1) For the dynamic set-cover problem, we maintain an \U0001D442(\U0001D4532)-approximately optimal solution in \U0001D442(\U0001D453⋅log(\U0001D45A+\U0001D45B)) amortized update time, where \U0001D453 is the maximum “frequency” of an element, \U0001D45B is the number of sets, and \U0001D45A is the maximum number of elements in the universe at any point in time. (2) For the dynamic \U0001D44F-matching problem, we maintain an \U0001D442(1)-approximately optimal solution in \U0001D442(log3\U0001D45B) amortized update time, where \U0001D45B is the number of nodes in the graph." alternative_title: - LNCS article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Giuseppe F. full_name: Italiano, Giuseppe F. last_name: Italiano citation: ama: 'Bhattacharya S, Henzinger MH, Italiano GF. Design of dynamic algorithms via primal-dual method. In: 42nd International Colloquium on Automata, Languages and Programming. Vol 9134. Springer Nature; 2015:206-218. doi:10.1007/978-3-662-47672-7_17' apa: 'Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2015). Design of dynamic algorithms via primal-dual method. In 42nd International Colloquium on Automata, Languages and Programming (Vol. 9134, pp. 206–218). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47672-7_17' chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Design of Dynamic Algorithms via Primal-Dual Method.” In 42nd International Colloquium on Automata, Languages and Programming, 9134:206–18. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47672-7_17. ieee: S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Design of dynamic algorithms via primal-dual method,” in 42nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 206–218. ista: 'Bhattacharya S, Henzinger MH, Italiano GF. 2015. Design of dynamic algorithms via primal-dual method. 42nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 9134, 206–218.' mla: Bhattacharya, Sayan, et al. “Design of Dynamic Algorithms via Primal-Dual Method.” 42nd International Colloquium on Automata, Languages and Programming, vol. 9134, Springer Nature, 2015, pp. 206–18, doi:10.1007/978-3-662-47672-7_17. short: S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 206–218. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2015-07-06 date_created: 2022-08-11T09:28:49Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-10T09:13:31Z day: '01' doi: 10.1007/978-3-662-47672-7_17 extern: '1' external_id: arxiv: - '1604.05337' intvolume: ' 9134' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.05337 month: '01' oa: 1 oa_version: Preprint page: 206 - 218 publication: 42nd International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - '9783662476710' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Design of dynamic algorithms via primal-dual method type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9134 year: '2015' ... --- _id: '11845' abstract: - lang: eng text: "Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.\r\nDepending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator–prey interactions between the species in a community to define viability constraints.\r\nDespite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.\r\nWe exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda." article_processing_charge: No article_type: original author: - first_name: Olga full_name: Chernomor, Olga last_name: Chernomor - first_name: Bui Quang full_name: Minh, Bui Quang last_name: Minh - first_name: Félix full_name: Forest, Félix last_name: Forest - first_name: Steffen full_name: Klaere, Steffen last_name: Klaere - first_name: Travis full_name: Ingram, Travis last_name: Ingram - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Arndt full_name: von Haeseler, Arndt last_name: von Haeseler citation: ama: Chernomor O, Minh BQ, Forest F, et al. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 2015;6(1):83-91. doi:10.1111/2041-210x.12299 apa: Chernomor, O., Minh, B. Q., Forest, F., Klaere, S., Ingram, T., Henzinger, M. H., & von Haeseler, A. (2015). Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. Wiley. https://doi.org/10.1111/2041-210x.12299 chicago: Chernomor, Olga, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika H Henzinger, and Arndt von Haeseler. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution. Wiley, 2015. https://doi.org/10.1111/2041-210x.12299. ieee: O. Chernomor et al., “Split diversity in constrained conservation prioritization using integer linear programming,” Methods in Ecology and Evolution, vol. 6, no. 1. Wiley, pp. 83–91, 2015. ista: Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger MH, von Haeseler A. 2015. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 6(1), 83–91. mla: Chernomor, Olga, et al. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution, vol. 6, no. 1, Wiley, 2015, pp. 83–91, doi:10.1111/2041-210x.12299. short: O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M.H. Henzinger, A. von Haeseler, Methods in Ecology and Evolution 6 (2015) 83–91. date_created: 2022-08-16T06:43:49Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-17T09:30:08Z day: '01' ddc: - '570' doi: 10.1111/2041-210x.12299 extern: '1' external_id: pmid: - '25893087' file: - access_level: open_access checksum: 880e78f09f0ac99cb351c48dc97623b6 content_type: application/pdf creator: asandaue date_created: 2022-08-16T06:52:53Z date_updated: 2022-08-16T06:52:53Z file_id: '11846' file_name: 2015_MethodsInEcologyAndEvolutionChernomor.pdf file_size: 411415 relation: main_file success: 1 file_date_updated: 2022-08-16T06:52:53Z has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 83-91 pmid: 1 publication: Methods in Ecology and Evolution publication_identifier: eissn: - 2041-210X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Split diversity in constrained conservation prioritization using integer linear programming 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: 6 year: '2015' ... --- _id: '11868' abstract: - lang: eng text: "Consider the following Online Boolean Matrix-Vector Multiplication problem: We are given an n x n matrix M and will receive n column-vectors of size n, denoted by v1, ..., vn, one by one. After seeing each vector vi, we have to output the product Mvi before we can see the next vector. A naive algorithm can solve this problem using O(n3) time in total, and its running time can be slightly improved to O(n3/log2 n) [Williams SODA'07]. We show that a conjecture that there is no truly subcubic (O(n3-ε)) time algorithm for this problem can be used to exhibit the underlying polynomial time hardness shared by many dynamic problems. For a number of problems, such as subgraph connectivity, Pagh's problem, d-failure connectivity, decremental single-source shortest paths, and decremental transitive closure, this conjecture implies tight hardness results. Thus, proving or disproving this conjecture will be very interesting as it will either imply several tight unconditional lower bounds or break through a common barrier that blocks progress with these problems. This conjecture might also be considered as strong evidence against any further improvement for these problems since refuting it will imply a major breakthrough for combinatorial Boolean matrix multiplication and other long-standing problems if the term \"combinatorial algorithms\" is interpreted as \"Strassen-like algorithms\" [Ballard et al. SPAA'11].\r\n\r\nThe conjecture also leads to hardness results for problems that were previously based on diverse problems and conjectures -- such as 3SUM, combinatorial Boolean matrix multiplication, triangle detection, and multiphase -- thus providing a uniform way to prove polynomial hardness results for dynamic algorithms; some of the new proofs are also simpler or even become trivial. The conjecture also leads to stronger and new, non-trivial, hardness results, e.g., for the fully-dynamic densest subgraph and diameter problems." article_number: 21-30 article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai - first_name: Thatchaphol full_name: Saranurak, Thatchaphol last_name: Saranurak citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015. doi:10.1145/2746539.2746609' apa: 'Henzinger, M. H., Krinninger, S., Nanongkai, D., & Saranurak, T. (2015). Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In 47th Annual ACM Symposium on Theory of Computing. Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746609' chicago: Henzinger, Monika H, Sebastian Krinninger, Danupon Nanongkai, and Thatchaphol Saranurak. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” In 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746609. ieee: M. H. Henzinger, S. Krinninger, D. Nanongkai, and T. Saranurak, “Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015. ista: 'Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. 2015. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 21–30.' mla: Henzinger, Monika H., et al. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” 47th Annual ACM Symposium on Theory of Computing, 21–30, Association for Computing Machinery, 2015, doi:10.1145/2746539.2746609. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, T. Saranurak, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015. conference: end_date: 2015-06-17 location: Portland, OR, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2015-06-14 date_created: 2022-08-16T09:31:21Z date_published: 2015-06-14T00:00:00Z date_updated: 2023-02-17T11:09:54Z day: '14' doi: 10.1145/2746539.2746609 extern: '1' external_id: arxiv: - '1511.06773' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.06773 month: '06' oa: 1 oa_version: Preprint publication: 47th Annual ACM Symposium on Theory of Computing publication_identifier: isbn: - 978-145033536-2 issn: - '0737.8017' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '11869' abstract: - lang: eng text: "While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of both time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a problem which lies at the core of many graph mining applications called densest subgraph problem. We develop an algorithm that achieves time- and space-efficiency for this problem simultaneously. It is one of the first of its kind for graph problems to the best of our knowledge.\r\n\r\nGiven an input graph, the densest subgraph is the subgraph that maximizes the ratio between the number of edges and the number of nodes. For any ε>0, our algorithm can, with high probability, maintain a (4+ε)-approximate solution under edge insertions and deletions using ~O(n) space and ~O(1) amortized time per update; here, $n$ is the number of nodes in the graph and ~O hides the O(polylog_{1+ε} n) term. The approximation ratio can be improved to (2+ε) with more time. It can be extended to a (2+ε)-approximation sublinear-time algorithm and a distributed-streaming algorithm. Our algorithm is the first streaming algorithm that can maintain the densest subgraph in one pass. Prior to this, no algorithm could do so even in the special case of an incremental stream and even when there is no time restriction. The previously best algorithm in this setting required O(log n) passes [BahmaniKV12]. The space required by our algorithm is tight up to a polylogarithmic factor." article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai - first_name: Charalampos full_name: Tsourakakis, Charalampos last_name: Tsourakakis citation: ama: 'Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015:173-182. doi:10.1145/2746539.2746592' apa: 'Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Tsourakakis, C. (2015). Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In 47th Annual ACM Symposium on Theory of Computing (pp. 173–182). Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746592' chicago: Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Charalampos Tsourakakis. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” In 47th Annual ACM Symposium on Theory of Computing, 173–82. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746592. ieee: S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and C. Tsourakakis, “Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015, pp. 173–182. ista: 'Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. 2015. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 173–182.' mla: Bhattacharya, Sayan, et al. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–82, doi:10.1145/2746539.2746592. short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, C. Tsourakakis, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–182. conference: end_date: 2015-06-17 location: Portland, OR, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2015-06-14 date_created: 2022-08-16T09:36:48Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-17T11:17:03Z day: '01' doi: 10.1145/2746539.2746592 extern: '1' external_id: arxiv: - '1504.02268' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.02268 month: '06' oa: 1 oa_version: Preprint page: 173 - 182 publication: 47th Annual ACM Symposium on Theory of Computing publication_identifier: isbn: - 978-145033536-2 issn: - 0737-8017 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '11837' abstract: - lang: eng text: "Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1-1/e). (2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation algorithm for 2-hop step function externalities. We also improve the result from [6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation algorithm." alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Wolfgang full_name: Dvorák, Wolfgang last_name: Dvorák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: ' Martin' full_name: Starnberger, Martin last_name: Starnberger citation: ama: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. Welfare maximization with friends-of-friends network externalities. In: 32nd International Symposium on Theoretical Aspects of Computer Science. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:90-102. doi:10.4230/LIPICS.STACS.2015.90' apa: 'Bhattacharya, S., Dvorák, W., Henzinger, M. H., & Starnberger, Martin. (2015). Welfare maximization with friends-of-friends network externalities. In 32nd International Symposium on Theoretical Aspects of Computer Science (Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2015.90' chicago: Bhattacharya, Sayan, Wolfgang Dvorák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” In 32nd International Symposium on Theoretical Aspects of Computer Science, 30:90–102. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPICS.STACS.2015.90. ieee: S. Bhattacharya, W. Dvorák, M. H. Henzinger, and Martin Starnberger, “Welfare maximization with friends-of-friends network externalities,” in 32nd International Symposium on Theoretical Aspects of Computer Science, Garching, Germany, 2015, vol. 30, pp. 90–102. ista: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. 2015. Welfare maximization with friends-of-friends network externalities. 32nd International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 30, 90–102.' mla: Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” 32nd International Symposium on Theoretical Aspects of Computer Science, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPICS.STACS.2015.90. short: S. Bhattacharya, W. Dvorák, M.H. Henzinger, Martin Starnberger, in:, 32nd International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102. conference: end_date: 2015-03-07 location: Garching, Germany name: 'STACS: Symposium on Theoretical Aspects of Computer Science' start_date: 2015-03-04 date_created: 2022-08-12T11:39:40Z date_published: 2015-02-26T00:00:00Z date_updated: 2023-02-21T16:32:37Z day: '26' doi: 10.4230/LIPICS.STACS.2015.90 extern: '1' intvolume: ' 30' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.STACS.2015.90 month: '02' oa: 1 oa_version: Published Version page: 90-102 publication: 32nd International Symposium on Theoretical Aspects of Computer Science publication_identifier: isbn: - 978-3-939897-78-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '11903' relation: later_version status: public scopus_import: '1' status: public title: Welfare maximization with friends-of-friends network externalities type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2015' ... --- _id: '11901' abstract: - lang: eng text: We consider auctions of indivisible items to unit-demand bidders with budgets. This setting was suggested as an expressive model for single sponsored search auctions. Prior work presented mechanisms that compute bidder-optimal outcomes and are truthful for a restricted set of inputs, i.e., inputs in so-called general position. This condition is easily violated. We provide the first mechanism that is truthful in expectation for all inputs and achieves for each bidder no worse utility than the bidder-optimal outcome. Additionally we give a complete characterization for which inputs mechanisms that compute bidder-optimal outcomes are truthful. article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: Henzinger MH, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 2015;573:1-15. doi:10.1016/j.tcs.2015.01.033 apa: Henzinger, M. H., & Loitzenbauer, V. (2015). Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.033 chicago: Henzinger, Monika H, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.033. ieee: M. H. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets revisited,” Theoretical Computer Science, vol. 573. Elsevier, pp. 1–15, 2015. ista: Henzinger MH, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 573, 1–15. mla: Henzinger, Monika H., and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science, vol. 573, Elsevier, 2015, pp. 1–15, doi:10.1016/j.tcs.2015.01.033. short: M.H. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015) 1–15. date_created: 2022-08-17T09:06:53Z date_published: 2015-03-30T00:00:00Z date_updated: 2023-02-17T14:50:04Z day: '30' doi: 10.1016/j.tcs.2015.01.033 extern: '1' intvolume: ' 573' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.tcs.2015.01.033 month: '03' oa: 1 oa_version: None page: 1-15 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Truthful unit-demand auctions with budgets revisited type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 573 year: '2015' ... --- _id: '11962' abstract: - lang: eng text: One of the rare alternative reagents for the reduction of carbon–carbon double bonds is diimide (HNNH), which can be generated in situ from hydrazine hydrate (N2H4⋅H2O) and O2. Although this selective method is extremely clean and powerful, it is rarely used, as the rate-determining oxidation of hydrazine in the absence of a catalyst is relatively slow using conventional batch protocols. A continuous high-temperature/high-pressure methodology dramatically enhances the initial oxidation step, at the same time allowing for a safe and scalable processing of the hazardous reaction mixture. Simple alkenes can be selectively reduced within 10–20 min at 100–120 °C and 20 bar O2 pressure. The development of a multi-injection reactor platform for the periodic addition of N2H4⋅H2O enables the reduction of less reactive olefins even at lower reaction temperatures. This concept was utilized for the highly selective reduction of artemisinic acid to dihydroartemisinic acid, the precursor molecule for the semisynthesis of the antimalarial drug artemisinin. The industrially relevant reduction was achieved by using four consecutive liquid feeds (of N2H4⋅H2O) and residence time units resulting in a highly selective reduction within approximately 40 min at 60 °C and 20 bar O2 pressure, providing dihydroartemisinic acid in ≥93 % yield and ≥95 % selectivity. article_processing_charge: No article_type: original author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Toma full_name: Glasnov, Toma last_name: Glasnov - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Pieber B, Glasnov T, Kappe CO. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 2015;21(11):4368-4376. doi:10.1002/chem.201406439 apa: Pieber, B., Glasnov, T., & Kappe, C. O. (2015). Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.201406439 chicago: Pieber, Bartholomäus, Toma Glasnov, and C. Oliver Kappe. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal. Wiley, 2015. https://doi.org/10.1002/chem.201406439. ieee: B. Pieber, T. Glasnov, and C. O. Kappe, “Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs,” Chemistry - A European Journal, vol. 21, no. 11. Wiley, pp. 4368–4376, 2015. ista: Pieber B, Glasnov T, Kappe CO. 2015. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 21(11), 4368–4376. mla: Pieber, Bartholomäus, et al. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal, vol. 21, no. 11, Wiley, 2015, pp. 4368–76, doi:10.1002/chem.201406439. short: B. Pieber, T. Glasnov, C.O. Kappe, Chemistry - A European Journal 21 (2015) 4368–4376. date_created: 2022-08-24T11:11:10Z date_published: 2015-03-09T00:00:00Z date_updated: 2023-02-21T10:09:30Z day: '09' doi: 10.1002/chem.201406439 extern: '1' external_id: pmid: - '25655090' intvolume: ' 21' issue: '11' language: - iso: eng month: '03' oa_version: None page: 4368-4376 pmid: 1 publication: Chemistry - A European Journal publication_identifier: eissn: - 1521-3765 issn: - 0947-6539 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2015' ... --- _id: '11977' abstract: - lang: eng text: The development of a continuous flow multistep strategy for the synthesis of linear peptoids and their subsequent macrocyclization via Click chemistry is described. The central transformation of this process is an Ugi four-component reaction generating the peptidomimetic core structure. In order to avoid exposure to the often toxic and malodorous isocyanide building blocks, the continuous approach was telescoped by the dehydration of the corresponding formamide. In a concurrent operation, the highly energetic azide moiety required for the subsequent intramolecular copper-catalyzed azide–alkyne cycloaddition (Click reaction) was installed by nucleophilic substitution from a bromide precursor. All steps yielding to the linear core structures can be conveniently coupled without the need for purification steps resulting in a single process generating the desired peptidomimetics in good to excellent yields within a 25 min reaction time. The following macrocyclization was realized in a coil reactor made of copper without any additional additive. A careful process intensification study demonstrated that this transformation occurs quantitatively within 25 min at 140 °C. Depending on the resulting ring strain, either a dimeric or a monomeric form of the cyclic product was obtained. article_processing_charge: No article_type: original author: - first_name: Carlos Eduardo M. full_name: Salvador, Carlos Eduardo M. last_name: Salvador - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Philipp M. full_name: Neu, Philipp M. last_name: Neu - first_name: Ana full_name: Torvisco, Ana last_name: Torvisco - first_name: Carlos full_name: Kleber Z. Andrade, Carlos last_name: Kleber Z. Andrade - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 2015;80(9):4590-4602. doi:10.1021/acs.joc.5b00445 apa: Salvador, C. E. M., Pieber, B., Neu, P. M., Torvisco, A., Kleber Z. Andrade, C., & Kappe, C. O. (2015). A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.joc.5b00445 chicago: Salvador, Carlos Eduardo M., Bartholomäus Pieber, Philipp M. Neu, Ana Torvisco, Carlos Kleber Z. Andrade, and C. Oliver Kappe. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.joc.5b00445. ieee: C. E. M. Salvador, B. Pieber, P. M. Neu, A. Torvisco, C. Kleber Z. Andrade, and C. O. Kappe, “A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids,” The Journal of Organic Chemistry, vol. 80, no. 9. American Chemical Society, pp. 4590–4602, 2015. ista: Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. 2015. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 80(9), 4590–4602. mla: Salvador, Carlos Eduardo M., et al. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry, vol. 80, no. 9, American Chemical Society, 2015, pp. 4590–602, doi:10.1021/acs.joc.5b00445. short: C.E.M. Salvador, B. Pieber, P.M. Neu, A. Torvisco, C. Kleber Z. Andrade, C.O. Kappe, The Journal of Organic Chemistry 80 (2015) 4590–4602. date_created: 2022-08-25T10:52:24Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-21T10:10:04Z day: '01' doi: 10.1021/acs.joc.5b00445 extern: '1' external_id: pmid: - '25842982' intvolume: ' 80' issue: '9' language: - iso: eng month: '05' oa_version: None page: 4590-4602 pmid: 1 publication: The Journal of Organic Chemistry publication_identifier: eissn: - 1520-6904 issn: - 0022-3263 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2015' ... --- _id: '11989' abstract: - lang: eng text: In recent years, the high demand for sustainable processes resulted in the development of highly attractive oxidation protocols utilizing molecular oxygen or even air instead of more uneconomic and often toxic reagents. The application of these sustainable, gaseous oxidants in conventional batch reactors is often associated with severe safety risks and process challenges especially on larger scales. Continuous flow technology offers the possibility to minimize these safety hazards and concurrently allows working in high-temperature/high-pressure regimes to access highly efficient oxidation protocols. This review article critically discusses recent literature examples of flow methodologies for selective aerobic oxidations of organic compounds. Several technologies and reactor designs for biphasic gas/liquid as well as supercritical reaction media are presented in detail. © Springer International Publishing Switzerland 2015. alternative_title: - Topics in Organometallic Chemistry article_processing_charge: No author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: 'Pieber B, Kappe CO. Aerobic oxidations in continuous flow. In: Noël T, ed. Organometallic Flow Chemistry. Vol 57. 1st ed. TOPORGAN. Cham: Springer Nature; 2015:97–136. doi:10.1007/3418_2015_133' apa: 'Pieber, B., & Kappe, C. O. (2015). Aerobic oxidations in continuous flow. In T. Noël (Ed.), Organometallic Flow Chemistry (1st ed., Vol. 57, pp. 97–136). Cham: Springer Nature. https://doi.org/10.1007/3418_2015_133' chicago: 'Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” In Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., 57:97–136. TOPORGAN. Cham: Springer Nature, 2015. https://doi.org/10.1007/3418_2015_133.' ieee: 'B. Pieber and C. O. Kappe, “Aerobic oxidations in continuous flow,” in Organometallic Flow Chemistry, 1st ed., vol. 57, T. Noël, Ed. Cham: Springer Nature, 2015, pp. 97–136.' ista: 'Pieber B, Kappe CO. 2015.Aerobic oxidations in continuous flow. In: Organometallic Flow Chemistry. Topics in Organometallic Chemistry, vol. 57, 97–136.' mla: Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., vol. 57, Springer Nature, 2015, pp. 97–136, doi:10.1007/3418_2015_133. short: B. Pieber, C.O. Kappe, in:, T. Noël (Ed.), Organometallic Flow Chemistry, 1st ed., Springer Nature, Cham, 2015, pp. 97–136. date_created: 2022-08-25T11:58:38Z date_published: 2015-06-10T00:00:00Z date_updated: 2023-02-21T10:10:35Z day: '10' doi: 10.1007/3418_2015_133 edition: '1' editor: - first_name: Timothy full_name: Noël, Timothy last_name: Noël extern: '1' intvolume: ' 57' language: - iso: eng month: '06' oa_version: None page: 97–136 place: Cham publication: Organometallic Flow Chemistry publication_identifier: eisbn: - '9783319332437' eissn: - 1616-8534 isbn: - '9783319332413' issn: - 1436-6002 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: TOPORGAN status: public title: Aerobic oxidations in continuous flow type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2015' ... --- _id: '120' abstract: - lang: eng text: Clustering of fine particles is of crucial importance in settings ranging from the early stages of planet formation to the coagulation of industrial powders and airborne pollutants. Models of such clustering typically focus on inelastic deformation and cohesion. However, even in charge-neutral particle systems comprising grains of the same dielectric material, tribocharging can generate large amounts of net positive or negative charge on individual particles, resulting in long-range electrostatic forces. The effects of such forces on cluster formation are not well understood and have so far not been studied in situ. Here we report the first observations of individual collide-and-capture events between charged submillimetre particles, including Kepler-like orbits. Charged particles can become trapped in their mutual electrostatic energy well and aggregate via multiple bounces. This enables the initiation of clustering at relative velocities much larger than the upper limit for sticking after a head-on collision, a long-standing issue known from pre-planetary dust aggregation. Moreover, Coulomb interactions together with dielectric polarization are found to stabilize characteristic molecule-like configurations, providing new insights for the modelling of clustering dynamics in a wide range of microscopic dielectric systems, such as charged polarizable ions, biomolecules and colloids. acknowledgement: This research was supported by NSF through DMR-1309611. The Chicago MRSEC, supported by NSF DMR-1420709, is gratefully acknowledged for access to its shared experimental facilities. author: - first_name: Victor full_name: Lee, Victor last_name: Lee - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Marc full_name: Miskin, Marc last_name: Miskin - first_name: Heinrich full_name: Jaeger, Heinrich last_name: Jaeger citation: ama: Lee V, Waitukaitis SR, Miskin M, Jaeger H. Direct observation of particle interactions and clustering in charged granular streams. Nature Physics. 2015;11(9):733-737. doi:10.1038/nphys3396 apa: Lee, V., Waitukaitis, S. R., Miskin, M., & Jaeger, H. (2015). Direct observation of particle interactions and clustering in charged granular streams. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3396 chicago: Lee, Victor, Scott R Waitukaitis, Marc Miskin, and Heinrich Jaeger. “Direct Observation of Particle Interactions and Clustering in Charged Granular Streams.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3396. ieee: V. Lee, S. R. Waitukaitis, M. Miskin, and H. Jaeger, “Direct observation of particle interactions and clustering in charged granular streams,” Nature Physics, vol. 11, no. 9. Nature Publishing Group, pp. 733–737, 2015. ista: Lee V, Waitukaitis SR, Miskin M, Jaeger H. 2015. Direct observation of particle interactions and clustering in charged granular streams. Nature Physics. 11(9), 733–737. mla: Lee, Victor, et al. “Direct Observation of Particle Interactions and Clustering in Charged Granular Streams.” Nature Physics, vol. 11, no. 9, Nature Publishing Group, 2015, pp. 733–37, doi:10.1038/nphys3396. short: V. Lee, S.R. Waitukaitis, M. Miskin, H. Jaeger, Nature Physics 11 (2015) 733–737. date_created: 2018-12-11T11:44:44Z date_published: 2015-07-13T00:00:00Z date_updated: 2021-01-12T06:49:02Z day: '13' doi: 10.1038/nphys3396 extern: '1' intvolume: ' 11' issue: '9' language: - iso: eng month: '07' oa_version: None page: 733 - 737 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7934' quality_controlled: '1' status: public title: Direct observation of particle interactions and clustering in charged granular streams type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '121' abstract: - lang: eng text: We show that the simplest building blocks of origami-based materials - rigid, degree-four vertices - are generically multistable. The existence of two distinct branches of folding motion emerging from the flat state suggests at least bistability, but we show how nonlinearities in the folding motions allow generic vertex geometries to have as many as five stable states. In special geometries with collinear folds and symmetry, more branches emerge leading to as many as six stable states. Tuning the fold energy parameters, we show how monostability is also possible. Finally, we show how to program the stability features of a single vertex into a periodic fold tessellation. The resulting metasheets provide a previously unanticipated functionality - tunable and switchable shape and size via multistability. acknowledgement: B. G. C. acknowledges support from FOM, and S. W. and M. v. H. acknowledge support from NWO. article_number: '055503' author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Rémi full_name: Menaut, Rémi last_name: Menaut - first_name: Bryan full_name: Chen, Bryan last_name: Chen - first_name: Martin full_name: Van Hecke, Martin last_name: Van Hecke citation: ama: 'Waitukaitis SR, Menaut R, Chen B, Van Hecke M. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 2015;114(5). doi:10.1103/PhysRevLett.114.055503' apa: 'Waitukaitis, S. R., Menaut, R., Chen, B., & Van Hecke, M. (2015). Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.055503' chicago: 'Waitukaitis, Scott R, Rémi Menaut, Bryan Chen, and Martin Van Hecke. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.055503.' ieee: 'S. R. Waitukaitis, R. Menaut, B. Chen, and M. Van Hecke, “Origami multistability: From single vertices to metasheets,” APS Physics, Physical Review Letters, vol. 114, no. 5. American Physical Society, 2015.' ista: 'Waitukaitis SR, Menaut R, Chen B, Van Hecke M. 2015. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 114(5), 055503.' mla: 'Waitukaitis, Scott R., et al. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters, vol. 114, no. 5, 055503, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.055503.' short: S.R. Waitukaitis, R. Menaut, B. Chen, M. Van Hecke, APS Physics, Physical Review Letters 114 (2015). date_created: 2018-12-11T11:44:44Z date_published: 2015-02-04T00:00:00Z date_updated: 2021-01-12T06:49:07Z day: '04' doi: 10.1103/PhysRevLett.114.055503 extern: '1' external_id: arxiv: - '1408.1607' intvolume: ' 114' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.1607 month: '02' oa: 1 oa_version: Preprint publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7933' quality_controlled: '1' status: public title: 'Origami multistability: From single vertices to metasheets' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2015' ... --- _id: '1311' abstract: - lang: eng text: In this paper, we develop an energy method to study finite speed of propagation and waiting time phenomena for the stochastic porous media equation with linear multiplicative noise in up to three spatial dimensions. Based on a novel iteration technique and on stochastic counterparts of weighted integral estimates used in the deterministic setting, we formulate a sufficient criterion on the growth of initial data which locally guarantees a waiting time phenomenon to occur almost surely. Up to a logarithmic factor, this criterion coincides with the optimal criterion known from the deterministic setting. Our technique can be modified to prove finite speed of propagation as well. acknowledgement: The first author has been supported by the Lithuanian-Swiss co- operation program under the project agreement No. CH-SMM-01/0. author: - first_name: Julian L full_name: Julian Fischer id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Günther full_name: Grün, Günther last_name: Grün citation: ama: 'Fischer JL, Grün G. Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical Analysis. 2015;47(1):825-854. doi:10.1137/140960578' apa: 'Fischer, J. L., & Grün, G. (2015). Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140960578' chicago: 'Fischer, Julian L, and Günther Grün. “Finite Speed of Propagation and Waiting Times for the Stochastic Porous Medium Equation: A Unifying Approach.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140960578.' ieee: 'J. L. Fischer and G. Grün, “Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach,” SIAM Journal on Mathematical Analysis, vol. 47, no. 1. Society for Industrial and Applied Mathematics , pp. 825–854, 2015.' ista: 'Fischer JL, Grün G. 2015. Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical Analysis. 47(1), 825–854.' mla: 'Fischer, Julian L., and Günther Grün. “Finite Speed of Propagation and Waiting Times for the Stochastic Porous Medium Equation: A Unifying Approach.” SIAM Journal on Mathematical Analysis, vol. 47, no. 1, Society for Industrial and Applied Mathematics , 2015, pp. 825–54, doi:10.1137/140960578.' short: J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 47 (2015) 825–854. date_created: 2018-12-11T11:51:18Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:49:48Z day: '01' doi: 10.1137/140960578 extern: 1 intvolume: ' 47' issue: '1' month: '01' page: 825 - 854 publication: SIAM Journal on Mathematical Analysis publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '5958' quality_controlled: 0 status: public title: 'Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach' type: journal_article volume: 47 year: '2015' ... --- _id: '1314' abstract: - lang: eng text: 'We derive a posteriori estimates for the modeling error caused by the assumption of perfect incompressibility in the incompressible Navier-Stokes equation: Real fluids are never perfectly incompressible but always feature at least some low amount of compressibility. Thus, their behavior is described by the compressible Navier-Stokes equation, the pressure being a steep function of the density. We rigorously estimate the difference between an approximate solution to the incompressible Navier-Stokes equation and any weak solution to the compressible Navier-Stokes equation in the sense of Lions (without assuming any additional regularity of solutions). Heuristics and numerical results suggest that our error estimates are of optimal order in the case of "well-behaved" flows and divergence-free approximations of the velocity field. Thus, we expect our estimates to justify the idealization of fluids as perfectly incompressible also in practical situations.' acknowledgement: The research of the author was supported by the Lithuanian-Swiss cooperation program under the project agreement CH-SMM-01/0. author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Fischer JL. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. 2015;53(5):2178-2205. doi:10.1137/140966654 apa: Fischer, J. L. (2015). A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140966654 chicago: Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140966654. ieee: J. L. Fischer, “A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation,” SIAM Journal on Numerical Analysis, vol. 53, no. 5. Society for Industrial and Applied Mathematics , pp. 2178–2205, 2015. ista: Fischer JL. 2015. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. 53(5), 2178–2205. mla: Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” SIAM Journal on Numerical Analysis, vol. 53, no. 5, Society for Industrial and Applied Mathematics , 2015, pp. 2178–205, doi:10.1137/140966654. short: J.L. Fischer, SIAM Journal on Numerical Analysis 53 (2015) 2178–2205. date_created: 2018-12-11T11:51:19Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:49:49Z day: '01' doi: 10.1137/140966654 extern: '1' intvolume: ' 53' issue: '5' language: - iso: eng month: '01' oa_version: None page: 2178 - 2205 publication: SIAM Journal on Numerical Analysis publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '5957' quality_controlled: '1' status: public title: A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2015' ... --- _id: '1313' abstract: - lang: eng text: We present an algorithm for the derivation of lower bounds on support propagation for a certain class of nonlinear parabolic equations. We proceed by combining the ideas in some recent papers by the author with the algorithmic construction of entropies due to Jüngel and Matthes, reducing the problem to a quantifier elimination problem. Due to its complexity, the quantifier elimination problem cannot be solved by present exact algorithms. However, by tackling the quantifier elimination problem numerically, in the case of the thin-film equation we are able to improve recent results by the author in the regime of strong slippage n ∈ (1, 2). For certain second-order doubly nonlinear parabolic equations, we are able to extend the known lower bounds on free boundary propagation to the case of irregular oscillatory initial data. Finally, we apply our method to a sixth-order quantum drift-diffusion equation, resulting in an upper bound on the time which it takes for the support to reach every point in the domain. acknowledgement: This research was supported by the Lithuanian-Swiss cooperation program under the project agreement No. CH-SMM-01/0. author: - first_name: Julian L full_name: Julian Fischer id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: 'Fischer JL. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. 2015;17(1):1-20. doi:10.4171/IFB/331' apa: 'Fischer, J. L. (2015). Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. European Mathematical Society Publishing House. https://doi.org/10.4171/IFB/331' chicago: 'Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” Interfaces and Free Boundaries. European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/IFB/331.' ieee: 'J. L. Fischer, “Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach,” Interfaces and Free Boundaries, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 1–20, 2015.' ista: 'Fischer JL. 2015. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. 17(1), 1–20.' mla: 'Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” Interfaces and Free Boundaries, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 1–20, doi:10.4171/IFB/331.' short: J.L. Fischer, Interfaces and Free Boundaries 17 (2015) 1–20. date_created: 2018-12-11T11:51:19Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:49:48Z day: '01' doi: 10.4171/IFB/331 extern: 1 intvolume: ' 17' issue: '1' month: '01' page: 1 - 20 publication: Interfaces and Free Boundaries publication_status: published publisher: European Mathematical Society Publishing House publist_id: '5956' quality_controlled: 0 status: public title: 'Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach' type: journal_article volume: 17 year: '2015' ... --- _id: '1316' abstract: - lang: eng text: In the present work we introduce the notion of a renormalized solution for reaction–diffusion systems with entropy-dissipating reactions. We establish the global existence of renormalized solutions. In the case of integrable reaction terms our notion of a renormalized solution reduces to the usual notion of a weak solution. Our existence result in particular covers all reaction–diffusion systems involving a single reversible reaction with mass-action kinetics and (possibly species-dependent) Fick-law diffusion; more generally, it covers the case of systems of reversible reactions with mass-action kinetics which satisfy the detailed balance condition. For such equations the existence of any kind of solution in general was an open problem, thereby motivating the study of renormalized solutions. acknowledgement: This research was supported by the Lithuanian-Swiss cooperation program under the project agreement No. CH-SMM-01/0. author: - first_name: Julian L full_name: Julian Fischer id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Fischer JL. Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. Archive for Rational Mechanics and Analysis. 2015;218(1):553-587. doi:10.1007/s00205-015-0866-x apa: Fischer, J. L. (2015). Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-015-0866-x chicago: Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating Reaction–Diffusion Systems.” Archive for Rational Mechanics and Analysis. Springer, 2015. https://doi.org/10.1007/s00205-015-0866-x. ieee: J. L. Fischer, “Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems,” Archive for Rational Mechanics and Analysis, vol. 218, no. 1. Springer, pp. 553–587, 2015. ista: Fischer JL. 2015. Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems. Archive for Rational Mechanics and Analysis. 218(1), 553–587. mla: Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating Reaction–Diffusion Systems.” Archive for Rational Mechanics and Analysis, vol. 218, no. 1, Springer, 2015, pp. 553–87, doi:10.1007/s00205-015-0866-x. short: J.L. Fischer, Archive for Rational Mechanics and Analysis 218 (2015) 553–587. date_created: 2018-12-11T11:51:20Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:49:50Z day: '01' doi: 10.1007/s00205-015-0866-x extern: 1 intvolume: ' 218' issue: '1' month: '10' page: 553 - 587 publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '5955' quality_controlled: 0 status: public title: Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems type: journal_article volume: 218 year: '2015' ... --- _id: '1383' abstract: - lang: eng text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants. article_number: '15094' article_processing_charge: No article_type: original author: - first_name: Luo full_name: Yu, Luo last_name: Yu - first_name: Stefan full_name: Scholl, Stefan last_name: Scholl - first_name: Anett full_name: Doering, Anett last_name: Doering - first_name: Zhang full_name: Yi, Zhang last_name: Yi - first_name: Niloufer full_name: Irani, Niloufer last_name: Irani - first_name: Simone full_name: Di Rubbo, Simone last_name: Di Rubbo - first_name: Lutz full_name: Neumetzler, Lutz last_name: Neumetzler - first_name: Praveen full_name: Krishnamoorthy, Praveen last_name: Krishnamoorthy - first_name: Isabelle full_name: Van Houtte, Isabelle last_name: Van Houtte - first_name: Evelien full_name: Mylle, Evelien last_name: Mylle - first_name: Volker full_name: Bischoff, Volker last_name: Bischoff - first_name: Samantha full_name: Vernhettes, Samantha last_name: Vernhettes - first_name: Johan full_name: Winne, Johan last_name: Winne - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: York full_name: Stierhof, York last_name: Stierhof - first_name: Karin full_name: Schumacher, Karin last_name: Schumacher - first_name: Staffan full_name: Persson, Staffan last_name: Persson - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94 apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94 chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94. ieee: L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015. ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094. mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94. short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015). date_created: 2018-12-11T11:51:42Z date_published: 2015-07-06T00:00:00Z date_updated: 2021-01-12T06:50:18Z day: '06' department: - _id: JiFr doi: 10.1038/nplants.2015.94 external_id: pmid: - '27250258' intvolume: ' 1' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/ month: '07' oa: 1 oa_version: Submitted Version pmid: 1 publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '5827' quality_controlled: '1' scopus_import: 1 status: public title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2015' ... --- _id: '1425' abstract: - lang: eng text: 'In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm.' alternative_title: - Advances in Neural Information Processing Systems author: - first_name: Anastasia full_name: Pentina, Anastasia id: 42E87FC6-F248-11E8-B48F-1D18A9856A87 last_name: Pentina - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems; 2015:1540-1548.' apa: 'Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.' chicago: Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015. ieee: 'A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.' ista: 'Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548.' mla: Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d. Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48. short: A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015, pp. 1540–1548. conference: end_date: 2015-12-12 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2015-12-07 date_created: 2018-12-11T11:51:57Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:50:39Z day: '01' department: - _id: ChLa ec_funded: 1 intvolume: ' 2015' language: - iso: eng main_file_link: - open_access: '1' url: http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks month: '01' oa: 1 oa_version: None page: 1540 - 1548 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: Neural Information Processing Systems publist_id: '5781' quality_controlled: '1' scopus_import: 1 status: public title: Lifelong learning with non-i.i.d. tasks type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2015 year: '2015' ... --- _id: '1424' abstract: - lang: eng text: We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data. acknowledgement: This work was partially supported by the Austrian Science FUnd, project no. KLI 00012. alternative_title: - Advances in Neural Information Processing Systems author: - first_name: Roland full_name: Kwitt, Roland last_name: Kwitt - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Marc full_name: Niethammer, Marc last_name: Niethammer - first_name: Weili full_name: Lin, Weili last_name: Lin - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 citation: ama: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.' apa: 'Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.' chicago: Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015. ieee: 'R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.' ista: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.' mla: Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78. short: R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078. conference: end_date: 2015-12-12 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2015-12-07 date_created: 2018-12-11T11:51:56Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:50:38Z day: '01' department: - _id: HeEd intvolume: ' 28' language: - iso: eng main_file_link: - open_access: '1' url: https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective month: '12' oa: 1 oa_version: Submitted Version page: 3070 - 3078 publication_status: published publisher: Neural Information Processing Systems publist_id: '5782' quality_controlled: '1' status: public title: Statistical topological data analysis-A kernel perspective type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2015' ... --- _id: '1430' abstract: - lang: eng text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient. author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Jorge full_name: Heredia, Jorge last_name: Heredia - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758' apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758' chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758. ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462. ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.' mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758. short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462. conference: end_date: 2015-07-15 location: Madrid, Spain name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2015-07-11 date_created: 2018-12-11T11:51:58Z date_published: 2015-07-11T00:00:00Z date_updated: 2021-01-12T06:50:41Z day: '11' department: - _id: NiBa - _id: CaGu doi: 10.1145/2739480.2754758 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.06260 month: '07' oa: 1 oa_version: Preprint page: 1455 - 1462 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation publication_status: published publisher: ACM publist_id: '5768' quality_controlled: '1' scopus_import: 1 status: public title: First steps towards a runtime comparison of natural and artificial evolution type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1474' abstract: - lang: eng text: Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data. article_processing_charge: No author: - first_name: Anna full_name: Ferrara, Anna last_name: Ferrara - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Bin full_name: Liu, Bin last_name: Liu - first_name: Bogdan full_name: Warinschi, Bogdan last_name: Warinschi citation: ama: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11' apa: 'Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11' chicago: Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11. ieee: 'A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic access control,” presented at the CSF: Computer Security Foundations, Verona, Italy, 2015, pp. 46–60.' ista: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic access control. CSF: Computer Security Foundations, 46–60.' mla: Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control. IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11. short: A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60. conference: end_date: 2015-07-17 location: Verona, Italy name: 'CSF: Computer Security Foundations' start_date: 2015-07-13 date_created: 2018-12-11T11:52:14Z date_published: 2015-09-04T00:00:00Z date_updated: 2021-01-12T06:50:59Z day: '04' department: - _id: KrPi doi: 10.1109/CSF.2015.11 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://epubs.surrey.ac.uk/808055/ month: '09' oa: 1 oa_version: Submitted Version page: 46-60 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: IEEE publist_id: '5722' quality_controlled: '1' status: public title: Policy privacy in cryptographic access control type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1473' abstract: - lang: eng text: In this paper we survey geometric and arithmetic techniques to study the cohomology of semiprojective hyperkähler manifolds including toric hyperkähler varieties, Nakajima quiver varieties and moduli spaces of Higgs bundles on Riemann surfaces. The resulting formulae for their Poincaré polynomials are combinatorial and representation theoretical in nature. In particular we will look at their Betti numbers and will establish some results and state some expectations on their asymptotic shape. author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Fernando full_name: Rodríguez Villegas, Fernando last_name: Rodríguez Villegas citation: ama: Hausel T, Rodríguez Villegas F. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015;2015(370):113-156. apa: Hausel, T., & Rodríguez Villegas, F. (2015). Cohomology of large semiprojective hyperkähler varieties. Asterisque. Societe Mathematique de France. chicago: Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque. Societe Mathematique de France, 2015. ieee: T. Hausel and F. Rodríguez Villegas, “Cohomology of large semiprojective hyperkähler varieties,” Asterisque, vol. 2015, no. 370. Societe Mathematique de France, pp. 113–156, 2015. ista: Hausel T, Rodríguez Villegas F. 2015. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015(370), 113–156. mla: Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque, vol. 2015, no. 370, Societe Mathematique de France, 2015, pp. 113–56. short: T. Hausel, F. Rodríguez Villegas, Asterisque 2015 (2015) 113–156. date_created: 2018-12-11T11:52:13Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:50:59Z day: '01' extern: 1 intvolume: ' 2015' issue: '370' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.4914 month: '01' oa: 1 page: 113 - 156 publication: Asterisque publication_status: published publisher: Societe Mathematique de France publist_id: '5723' quality_controlled: 0 status: public title: Cohomology of large semiprojective hyperkähler varieties type: review volume: 2015 year: '2015' ... --- _id: '1483' abstract: - lang: eng text: Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes. author: - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Roland full_name: Kwitt, Roland last_name: Kwitt citation: ama: 'Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106' apa: 'Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106' chicago: Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106. ieee: 'J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.' ista: 'Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748.' mla: Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106. short: J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748. conference: end_date: 2015-06-12 location: Boston, MA, USA name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2015-06-07 date_created: 2018-12-11T11:52:17Z date_published: 2015-10-14T00:00:00Z date_updated: 2021-01-12T06:51:03Z day: '14' department: - _id: HeEd doi: 10.1109/CVPR.2015.7299106 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1412.6821 month: '10' oa: 1 oa_version: Preprint page: 4741 - 4748 publication_identifier: eisbn: - '978-1-4673-6964-0 ' publication_status: published publisher: IEEE publist_id: '5709' scopus_import: 1 status: public title: A stable multi-scale kernel for topological machine learning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1498' abstract: - lang: eng text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea. alternative_title: - LIPIcs author: - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90 apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90' chicago: Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90. ieee: C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015. ista: Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102. mla: Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90. short: C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102. conference: end_date: 2015-05-06 location: Asilomar, CA, United States name: 'SNAPL: Summit oN Advances in Programming Languages' start_date: 2015-05-03 date_created: 2018-12-11T11:52:22Z date_published: 2015-01-01T00:00:00Z date_updated: 2020-08-11T10:09:14Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.4230/LIPIcs.SNAPL.2015.90 ec_funded: 1 file: - access_level: open_access checksum: cf5e94baa89a2dc4c5de01abc676eda8 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:02Z date_updated: 2020-07-14T12:44:58Z file_id: '5050' file_name: IST-2016-499-v1+1_9.pdf file_size: 489362 relation: main_file file_date_updated: 2020-07-14T12:44:58Z has_accepted_license: '1' intvolume: ' 32' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 90 - 102 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - '978-3-939897-80-4 ' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5681' pubrep_id: '499' quality_controlled: '1' scopus_import: 1 series_title: Leibniz International Proceedings in Informatics status: public title: The need for language support for fault-tolerant distributed 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2015' ... --- _id: '1497' abstract: - lang: eng text: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide. acknowledgement: "Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna." article_number: e146 author: - first_name: Daniel full_name: Andergassen, Daniel last_name: Andergassen - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter - first_name: Tomasz full_name: Kulinski, Tomasz last_name: Kulinski - first_name: Philipp full_name: Guenzl, Philipp last_name: Guenzl - first_name: Philipp full_name: Bammer, Philipp last_name: Bammer - first_name: Denise full_name: Barlow, Denise last_name: Barlow - first_name: Florian full_name: Pauler, Florian last_name: Pauler - first_name: Quanah full_name: Hudson, Quanah last_name: Hudson citation: ama: Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 2015;43(21). doi:10.1093/nar/gkv727 apa: Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv727 chicago: Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727. ieee: D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” Nucleic Acids Research, vol. 43, no. 21. Oxford University Press, 2015. ista: Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146. mla: Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727. short: D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015). date_created: 2018-12-11T11:52:22Z date_published: 2015-07-21T00:00:00Z date_updated: 2021-01-12T06:51:09Z day: '21' ddc: - '570' department: - _id: GaNo doi: 10.1093/nar/gkv727 file: - access_level: open_access checksum: 385b83854fd0eb2e4f386867da2823e2 content_type: application/pdf creator: dernst date_created: 2018-12-20T14:18:57Z date_updated: 2020-07-14T12:44:58Z file_id: '5768' file_name: 2015_NucleicAcidsRes_Andergassen.pdf file_size: 6863297 relation: main_file file_date_updated: 2020-07-14T12:44:58Z has_accepted_license: '1' intvolume: ' 43' issue: '21' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nucleic Acids Research publication_status: published publisher: Oxford University Press publist_id: '5682' quality_controlled: '1' scopus_import: 1 status: public title: Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data 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: 43 year: '2015' ... --- _id: '1499' abstract: - lang: eng text: "We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata." acknowledgement: "The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734." alternative_title: - LIPIcs author: - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Kim full_name: Larsen, Kim last_name: Larsen - first_name: Simon full_name: Laursen, Simon last_name: Laursen - first_name: Jiří full_name: Srba, Jiří last_name: Srba citation: ama: 'Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142' apa: 'Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142' chicago: Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142. ieee: 'J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.' ista: 'Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.' mla: Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142. short: J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154. conference: end_date: 2015-09-04 location: Madrid, Spain name: 'CONCUR: Concurrency Theory' start_date: 2015-09-01 date_created: 2018-12-11T11:52:22Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:51:10Z day: '01' ddc: - '000' - '003' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2015.142 ec_funded: 1 file: - access_level: open_access checksum: 49eb5021caafaabe5356c65b9c5f8c9c content_type: application/pdf creator: system date_created: 2018-12-12T10:08:12Z date_updated: 2020-07-14T12:44:58Z file_id: '4672' file_name: IST-2016-498-v1+1_32.pdf file_size: 623563 relation: main_file file_date_updated: 2020-07-14T12:44:58Z has_accepted_license: '1' intvolume: ' 42' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 142 - 154 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5680' pubrep_id: '498' quality_controlled: '1' scopus_import: 1 status: public title: Polynomial time decidability of weighted synchronization under partial observability 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: 42 year: '2015' ... --- _id: '1495' abstract: - lang: eng text: 'Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. ' author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham - first_name: Vitaliy full_name: Kurlin, Vitaliy last_name: Kurlin citation: ama: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings of the 27th Canadian Conference on Computational Geometry. Vol 2015-August. Queen’s University; 2015:128-135.' apa: 'Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk packing. In Proceedings of the 27th Canadian Conference on Computational Geometry (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.' chicago: Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational Geometry, 2015–August:128–35. Queen’s University, 2015. ieee: H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in Proceedings of the 27th Canadian Conference on Computational Geometry, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135. ista: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.' mla: Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the 27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s University, 2015, pp. 128–35. short: H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135. conference: end_date: 2015-08-12 location: Ontario, Canada name: 'CCCG: Canadian Conference on Computational Geometry' start_date: 2015-08-10 date_created: 2018-12-11T11:52:21Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:09Z day: '01' department: - _id: HeEd ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1505.03402 month: '08' oa: 1 oa_version: Submitted Version page: 128-135 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Proceedings of the 27th Canadian Conference on Computational Geometry publication_status: published publisher: Queen's University publist_id: '5684' quality_controlled: '1' scopus_import: 1 status: public title: Relaxed disk packing type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2015-August year: '2015' ... --- _id: '1504' abstract: - lang: eng text: Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones. author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: Liang full_name: Lin, Liang last_name: Lin - first_name: Guangming full_name: Pan, Guangming last_name: Pan - first_name: Wang full_name: Zhou, Wang last_name: Zhou citation: ama: Bao Z, Lin L, Pan G, Zhou W. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 2015;43(6):2588-2623. doi:10.1214/15-AOS1353 apa: Bao, Z., Lin, L., Pan, G., & Zhou, W. (2015). Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AOS1353 chicago: Bao, Zhigang, Liang Lin, Guangming Pan, and Wang Zhou. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/15-AOS1353. ieee: Z. Bao, L. Lin, G. Pan, and W. Zhou, “Spectral statistics of large dimensional spearman s rank correlation matrix and its application,” Annals of Statistics, vol. 43, no. 6. Institute of Mathematical Statistics, pp. 2588–2623, 2015. ista: Bao Z, Lin L, Pan G, Zhou W. 2015. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 43(6), 2588–2623. mla: Bao, Zhigang, et al. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics, vol. 43, no. 6, Institute of Mathematical Statistics, 2015, pp. 2588–623, doi:10.1214/15-AOS1353. short: Z. Bao, L. Lin, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 2588–2623. date_created: 2018-12-11T11:52:24Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:14Z day: '01' doi: 10.1214/15-AOS1353 extern: '1' intvolume: ' 43' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1312.5119 month: '12' oa: 1 oa_version: Published Version page: 2588 - 2623 publication: Annals of Statistics publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5674' quality_controlled: '1' status: public title: Spectral statistics of large dimensional spearman s rank correlation matrix and its application type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2015' ... --- _id: '1500' abstract: - lang: eng text: In this poster, we present methods for randomly generating hybrid automata with affine differential equations, invariants, guards, and assignments. Selecting an arbitrary affine function from the set of all affine functions results in a low likelihood of generating hybrid automata with diverse and interesting behaviors, as there are an uncountable number of elements in the set of all affine functions. Instead, we partition the set of all affine functions into potentially interesting classes and randomly select elements from these classes. For example, we partition the set of all affine differential equations by using restrictions on eigenvalues such as those that yield stable, unstable, etc. equilibrium points. We partition the components describing discrete behavior (guards, assignments, and invariants) to allow either time-dependent or state-dependent switching, and in particular provide the ability to generate subclasses of piecewise-affine hybrid automata. Our preliminary experimental results with a prototype tool called HyRG (Hybrid Random Generator) illustrate the feasibility of this generation method to automatically create standard hybrid automaton examples like the bouncing ball and thermostat. alternative_title: - '18th ACM International Conference on Hybrid Systems: Computation and Control, HSCC 2015' author: - first_name: Luan full_name: Nguyen, Luan V last_name: Nguyen - first_name: Christian full_name: Christian Schilling id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Sergiy full_name: Sergiy Bogomolov id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Taylor full_name: Johnson, Taylor T last_name: Johnson citation: ama: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata. Springer; 2015:289-290. doi:10.1145/2728606.2728650' apa: 'Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Poster: HyRG: A random generation tool for affine hybrid automata. HSCC: Hybrid Systems - Computation and Control (pp. 289–290). Springer. https://doi.org/10.1145/2728606.2728650' chicago: 'Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata. HSCC: Hybrid Systems - Computation and Control. Springer, 2015. https://doi.org/10.1145/2728606.2728650.' ieee: 'L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, Poster: HyRG: A random generation tool for affine hybrid automata. Springer, 2015, pp. 289–290.' ista: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Poster: HyRG: A random generation tool for affine hybrid automata, Springer,p.' mla: 'Nguyen, Luan, et al. “Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata.” HSCC: Hybrid Systems - Computation and Control, Springer, 2015, pp. 289–90, doi:10.1145/2728606.2728650.' short: 'L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, Poster: HyRG: A Random Generation Tool for Affine Hybrid Automata, Springer, 2015.' date_created: 2018-12-11T11:52:23Z date_published: 2015-04-14T00:00:00Z date_updated: 2019-04-26T07:22:03Z day: '14' doi: 10.1145/2728606.2728650 extern: 1 month: '04' page: 289 - 290 publication: 'HSCC: Hybrid Systems - Computation and Control' publication_status: published publisher: Springer publist_id: '5678' quality_controlled: 0 status: public title: 'Poster: HyRG: A random generation tool for affine hybrid automata' type: conference_poster year: '2015' ... --- _id: '1503' abstract: - lang: eng text: A Herman-Avila-Bochi type formula is obtained for the average sum of the top d Lyapunov exponents over a one-parameter family of double-struck G-cocycles, where double-struck G is the group that leaves a certain, non-degenerate Hermitian form of signature (c, d) invariant. The generic example of such a group is the pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group HSp(2d) which naturally appears for cocycles related to Schrödinger operators. In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi formula for SL(2, ℝ) cocycles. author: - first_name: Christian full_name: Sadel, Christian id: 4760E9F8-F248-11E8-B48F-1D18A9856A87 last_name: Sadel orcid: 0000-0001-8255-3968 citation: ama: Sadel C. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 2015;35(5):1582-1591. doi:10.1017/etds.2013.103 apa: Sadel, C. (2015). A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2013.103 chicago: Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2015. https://doi.org/10.1017/etds.2013.103. ieee: C. Sadel, “A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles,” Ergodic Theory and Dynamical Systems, vol. 35, no. 5. Cambridge University Press, pp. 1582–1591, 2015. ista: Sadel C. 2015. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 35(5), 1582–1591. mla: Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems, vol. 35, no. 5, Cambridge University Press, 2015, pp. 1582–91, doi:10.1017/etds.2013.103. short: C. Sadel, Ergodic Theory and Dynamical Systems 35 (2015) 1582–1591. date_created: 2018-12-11T11:52:24Z date_published: 2015-03-14T00:00:00Z date_updated: 2021-01-12T06:51:13Z day: '14' doi: 10.1017/etds.2013.103 extern: '1' intvolume: ' 35' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1307.8414 month: '03' oa: 1 oa_version: Preprint page: 1582 - 1591 publication: Ergodic Theory and Dynamical Systems publication_status: published publisher: Cambridge University Press publist_id: '5675' quality_controlled: '1' status: public title: A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2015' ... --- _id: '1510' abstract: - lang: eng text: 'The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f'' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. ' alternative_title: - LIPIcs author: - first_name: Peter full_name: Franek, Peter id: 473294AE-F248-11E8-B48F-1D18A9856A87 last_name: Franek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál citation: ama: 'Franek P, Krcál M. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842' apa: 'Franek, P., & Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.842' chicago: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842. ieee: 'P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856.' ista: 'Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.' mla: Franek, Peter, and Marek Krcál. On Computability and Triviality of Well Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842. short: P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856. conference: end_date: 2015-06-25 location: Eindhoven, Netherlands name: 'SoCG: Symposium on Computational Geometry' start_date: 2015-06-22 date_created: 2018-12-11T11:52:26Z date_published: 2015-06-11T00:00:00Z date_updated: 2023-02-21T17:02:57Z day: '11' ddc: - '510' department: - _id: UlWa - _id: HeEd doi: 10.4230/LIPIcs.SOCG.2015.842 ec_funded: 1 file: - access_level: open_access checksum: 49eb5021caafaabe5356c65b9c5f8c9c content_type: application/pdf creator: system date_created: 2018-12-12T10:13:19Z date_updated: 2020-07-14T12:44:59Z file_id: '5001' file_name: IST-2016-503-v1+1_32.pdf file_size: 623563 relation: main_file file_date_updated: 2020-07-14T12:44:59Z has_accepted_license: '1' intvolume: ' 34' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 842 - 856 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5667' pubrep_id: '503' quality_controlled: '1' related_material: record: - id: '1408' relation: later_version status: public scopus_import: 1 status: public title: On computability and triviality of well 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1505' abstract: - lang: eng text: This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed. acknowledgement: "B.Z. was supported in part by NSFC Grant 11071213, ZJNSF \ Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported \ in part by the Ministry of Education, Singapore, under Grant ARC 14/11, \ and by a Grant R-155-000-131-112 at the National University of Singapore\r\n" author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: Guangming full_name: Pan, Guangming last_name: Pan - first_name: Wang full_name: Zhou, Wang last_name: Zhou citation: ama: Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 2015;43(1):382-421. doi:10.1214/14-AOS1281 apa: Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281 chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281. ieee: Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” Annals of Statistics, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015. ista: Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421. mla: Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281. short: Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421. date_created: 2018-12-11T11:52:25Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:51:14Z day: '01' department: - _id: LaEr doi: 10.1214/14-AOS1281 intvolume: ' 43' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1304.5690 month: '02' oa: 1 oa_version: Preprint page: 382 - 421 publication: Annals of Statistics publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5672' quality_controlled: '1' status: public title: Universality for the largest eigenvalue of sample covariance matrices with general population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2015' ... --- _id: '1508' abstract: - lang: eng text: We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Horng full_name: Yau, Horng last_name: Yau citation: ama: Erdös L, Yau H. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548 apa: Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/548 chicago: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society. European Mathematical Society, 2015. https://doi.org/10.4171/JEMS/548. ieee: L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” Journal of the European Mathematical Society, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015. ista: Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036. mla: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548. short: L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036. date_created: 2018-12-11T11:52:26Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:15Z day: '01' department: - _id: LaEr doi: 10.4171/JEMS/548 intvolume: ' 17' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1211.3786 month: '08' oa: 1 oa_version: Preprint page: 1927 - 2036 publication: Journal of the European Mathematical Society publication_status: published publisher: European Mathematical Society publist_id: '5669' quality_controlled: '1' scopus_import: 1 status: public title: Gap universality of generalized Wigner and β ensembles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1506' abstract: - lang: eng text: Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1). author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: Guangming full_name: Pan, Guangming last_name: Pan - first_name: Wang full_name: Zhou, Wang last_name: Zhou citation: ama: Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli. 2015;21(3):1600-1628. doi:10.3150/14-BEJ615 apa: Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/14-BEJ615 chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2015. https://doi.org/10.3150/14-BEJ615. ieee: Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015. ista: Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628. mla: Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:10.3150/14-BEJ615. short: Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628. date_created: 2018-12-11T11:52:25Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:14Z day: '01' department: - _id: LaEr doi: 10.3150/14-BEJ615 intvolume: ' 21' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1208.5823 month: '08' oa: 1 oa_version: Preprint page: 1600 - 1628 publication: Bernoulli publication_status: published publisher: Bernoulli Society for Mathematical Statistics and Probability publist_id: '5671' quality_controlled: '1' status: public title: The logarithmic law of random determinant type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2015' ... --- _id: '1513' abstract: - lang: eng text: "Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. " article_processing_charge: No author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: 'Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268. doi:10.1093/gbe/evv215' apa: 'Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215' chicago: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.' ieee: 'A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” Genome Biology and Evolution, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.' ista: 'Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.' mla: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.' short: A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268. date_created: 2018-12-11T11:52:27Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:18Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evv215 ec_funded: 1 file: - access_level: open_access checksum: 2b56b8c2e2a1d4cc3c9cb8daba26dd9b content_type: application/pdf creator: system date_created: 2018-12-12T10:17:29Z date_updated: 2020-07-14T12:45:00Z file_id: '5284' file_name: IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf file_size: 858027 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 7' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 3259 - 3268 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5664' pubrep_id: '496' quality_controlled: '1' scopus_import: 1 status: public title: 'The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2015' ... --- _id: '1517' abstract: - lang: eng text: "We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n" article_number: '89' 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: Michiel full_name: Renger, Michiel last_name: Renger citation: ama: Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 2015;20. doi:10.1214/ECP.v20-4315 apa: Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315 chicago: Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315. ieee: M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” Electronic Communications in Probability, vol. 20. Institute of Mathematical Statistics, 2015. ista: Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89. mla: Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315. short: M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015). date_created: 2018-12-11T11:52:29Z date_published: 2015-11-29T00:00:00Z date_updated: 2021-01-12T06:51:19Z day: '29' ddc: - '519' department: - _id: JaMa doi: 10.1214/ECP.v20-4315 file: - access_level: open_access checksum: 135741c17d3e1547ca696b6fbdcd559c content_type: application/pdf creator: system date_created: 2018-12-12T10:10:39Z date_updated: 2020-07-14T12:45:00Z file_id: '4828' file_name: IST-2016-494-v1+1_4315-23820-1-PB.pdf file_size: 230525 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 20' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Electronic Communications in Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5660' pubrep_id: '494' quality_controlled: '1' scopus_import: 1 status: public title: From large deviations to Wasserstein gradient flows in multiple dimensions 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2015' ... --- _id: '1515' abstract: - lang: eng text: Type 1 metabotropic glutamate (mGlu1) receptors play a pivotal role in different forms of synaptic plasticity in the cerebellar cortex, e.g. long-term depression at glutamatergic synapses and rebound potentiation at GABAergic synapses. These various forms of plasticity might depend on the subsynaptic arrangement of the receptor in Purkinje cells that can be regulated by protein-protein interactions. This study investigated, by means of the freeze-fracture replica immunogold labelling method, the subcellular localization of mGlu1 receptors in the rodent cerebellum and whether Homer proteins regulate their subsynaptic distribution. We observed a widespread extrasynaptic localization of mGlu1 receptors and confirmed their peri-synaptic enrichment at glutamatergic synapses. Conversely, we detected mGlu1 receptors within the main body of GABAergic synapses onto Purkinje cell dendrites. Although Homer proteins are known to interact with the mGlu1 receptor C-terminus, we could not detect Homer3, the most abundant Homer protein in the cerebellar cortex, at GABAergic synapses by pre-embedding and post-embedding immunoelectron microscopy. We then hypothesized a critical role for Homer proteins in the peri-junctional localization of mGlu1 receptors at glutamatergic synapses. To disrupt Homer-associated protein complexes, mice were tail-vein injected with the membrane-permeable dominant-negative TAT-Homer1a. Freeze-fracture replica immunogold labelling analysis showed no significant alteration in the mGlu1 receptor distribution pattern at parallel fibre-Purkinje cell synapses, suggesting that other scaffolding proteins are involved in the peri-synaptic confinement. The identification of interactors that regulate the subsynaptic localization of the mGlu1 receptor at neurochemically distinct synapses may offer new insight into its trafficking and intracellular signalling. acknowledgement: This work was supported by the Austrian Science Fund (FWF) (project W012060-10 to F.F.), The Japan Society for the Promotion of Science (JSPS) (to R.S.) and Agence Nationale de la Recherche (ANR-11-BSV4-018-03, DELTAPLAN), Région Languedoc-Roussillon (Chercheur d’Avenir) (to J.P.). The authors thank S. Schönherr for excellent technical support and Dr Furuichi for kindly providing anti-Homer3 antibodies. author: - first_name: Mahnaz full_name: Mansouri, Mahnaz last_name: Mansouri - first_name: Yu full_name: Kasugai, Yu last_name: Kasugai - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Federica full_name: Bertaso, Federica last_name: Bertaso - first_name: Fabrice full_name: Raynaud, Fabrice last_name: Raynaud - first_name: Julie full_name: Perroy, Julie last_name: Perroy - first_name: Laurent full_name: Fagni, Laurent last_name: Fagni - first_name: Walter full_name: Walter Kaufmann id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Francesco full_name: Ferraguti, Francesco last_name: Ferraguti citation: ama: Mansouri M, Kasugai Y, Fukazawa Y, et al. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. 2015;41(2):157-167. doi:10.1111/ejn.12779 apa: Mansouri, M., Kasugai, Y., Fukazawa, Y., Bertaso, F., Raynaud, F., Perroy, J., … Ferraguti, F. (2015). Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.12779 chicago: Mansouri, Mahnaz, Yu Kasugai, Yugo Fukazawa, Federica Bertaso, Fabrice Raynaud, Julie Perroy, Laurent Fagni, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” European Journal of Neuroscience. Wiley-Blackwell, 2015. https://doi.org/10.1111/ejn.12779. ieee: M. Mansouri et al., “Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex,” European Journal of Neuroscience, vol. 41, no. 2. Wiley-Blackwell, pp. 157–167, 2015. ista: Mansouri M, Kasugai Y, Fukazawa Y, Bertaso F, Raynaud F, Perroy J, Fagni L, Kaufmann W, Watanabe M, Shigemoto R, Ferraguti F. 2015. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. 41(2), 157–167. mla: Mansouri, Mahnaz, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” European Journal of Neuroscience, vol. 41, no. 2, Wiley-Blackwell, 2015, pp. 157–67, doi:10.1111/ejn.12779. short: M. Mansouri, Y. Kasugai, Y. Fukazawa, F. Bertaso, F. Raynaud, J. Perroy, L. Fagni, W. Kaufmann, M. Watanabe, R. Shigemoto, F. Ferraguti, European Journal of Neuroscience 41 (2015) 157–167. date_created: 2018-12-11T11:52:28Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T10:02:24Z day: '01' doi: 10.1111/ejn.12779 extern: 1 intvolume: ' 41' issue: '2' month: '01' page: 157 - 167 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '5662' quality_controlled: 0 status: public title: Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex 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 volume: 41 year: '2015' ... --- _id: '1514' abstract: - lang: eng text: 'Endocannabinoids (eCBs) play key roles in brain function, acting as modulatory signals in synaptic transmission and plasticity. They are recognized as retrograde messengers that mediate long-term synaptic depression (LTD), but their ability to induce long-term potentiation (LTP) is poorly known. We show that eCBs induce the long-term enhancement of transmitter release at single hippocampal synapses through stimulation of astrocytes when coincident with postsynaptic activity. This LTP requires the coordinated activity of the 3 elements of the tripartite synapse: 1) eCB-evoked astrocyte calcium signal that stimulates glutamate release; 2) postsynaptic nitric oxide production; and 3) activation of protein kinase C and presynaptic group I metabotropic glutamate receptors, whose location at presynaptic sites was confirmed by immunoelectron microscopy. Hence, while eCBs act as retrograde signals to depress homoneuronal synapses, they serve as lateral messengers to induce LTP in distant heteroneuronal synapses through stimulation of astrocytes. Therefore, eCBs can trigger LTP through stimulation of astrocyte-neuron signaling, revealing novel cellular mechanisms of eCB effects on synaptic plasticity.' acknowledgement: |- This work was supported by grants from Ministerio de Economia y Competitividad, Spain (MINECO; BFU2010-15832), European Union (HEALTH-F2-2007-202167), and Cajal Blue Brain to A.A. Grants from Spain (MINECO; BFU-2009-08404 and CSD2008-00005) to R.L. Grants from Spain (MINECO; Consolider, CSD2010-00045; Ramón y Cajal Program, RYC-2012-12014; and BFU2013-47265) to G.P. We thank Dr Atsu Aiba (Animal Resources, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo) for the donation of the mGluR1b rescue mice. author: - first_name: Marta full_name: Gómez-Gonzalo, Marta last_name: Gómez Gonzalo - first_name: Marta full_name: Navarrete, Marta last_name: Navarrete - first_name: Gertrudis full_name: Perea, Gertrudis last_name: Perea - first_name: Ana full_name: Covelo, Ana last_name: Covelo - first_name: Mario full_name: Martín-Fernández, Mario last_name: Martín Fernández - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Alfonso full_name: Araque, Alfonso last_name: Araque citation: ama: Gómez Gonzalo M, Navarrete M, Perea G, et al. Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. 2015;25(10):3699-3712. doi:10.1093/cercor/bhu231 apa: Gómez Gonzalo, M., Navarrete, M., Perea, G., Covelo, A., Martín Fernández, M., Shigemoto, R., … Araque, A. (2015). Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhu231 chicago: Gómez Gonzalo, Marta, Marta Navarrete, Gertrudis Perea, Ana Covelo, Mario Martín Fernández, Ryuichi Shigemoto, Rafael Luján, and Alfonso Araque. “Endocannabinoids Induce Lateral Long Term Potentiation of Transmitter Release by Stimulation of Gliotransmission.” Cerebral Cortex. Oxford University Press, 2015. https://doi.org/10.1093/cercor/bhu231. ieee: M. Gómez Gonzalo et al., “Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission,” Cerebral Cortex, vol. 25, no. 10. Oxford University Press, pp. 3699–3712, 2015. ista: Gómez Gonzalo M, Navarrete M, Perea G, Covelo A, Martín Fernández M, Shigemoto R, Luján R, Araque A. 2015. Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission. Cerebral Cortex. 25(10), 3699–3712. mla: Gómez Gonzalo, Marta, et al. “Endocannabinoids Induce Lateral Long Term Potentiation of Transmitter Release by Stimulation of Gliotransmission.” Cerebral Cortex, vol. 25, no. 10, Oxford University Press, 2015, pp. 3699–712, doi:10.1093/cercor/bhu231. short: M. Gómez Gonzalo, M. Navarrete, G. Perea, A. Covelo, M. Martín Fernández, R. Shigemoto, R. Luján, A. Araque, Cerebral Cortex 25 (2015) 3699–3712. date_created: 2018-12-11T11:52:27Z date_published: 2015-10-10T00:00:00Z date_updated: 2021-01-12T06:51:18Z day: '10' doi: 10.1093/cercor/bhu231 extern: 1 intvolume: ' 25' issue: '10' month: '10' page: 3699 - 3712 publication: Cerebral Cortex publication_status: published publisher: Oxford University Press publist_id: '5663' quality_controlled: 0 status: public title: Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission type: journal_article volume: 25 year: '2015' ... --- _id: '1519' abstract: - lang: eng text: Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so. author: - 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: Maria full_name: Servedio, Maria last_name: Servedio citation: ama: Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641 apa: Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641 chicago: Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641. ieee: N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015. ista: Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112. mla: Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641. short: N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112. date_created: 2018-12-11T11:52:29Z date_published: 2015-03-19T00:00:00Z date_updated: 2021-01-12T06:51:20Z day: '19' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.12641 ec_funded: 1 file: - access_level: open_access checksum: fd8d23f476bc194419929b72ca265c02 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:34Z date_updated: 2020-07-14T12:45:00Z file_id: '4822' file_name: IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf file_size: 188872 relation: main_file - access_level: open_access checksum: b774911e70044641d556e258efcb52ef content_type: application/pdf creator: system date_created: 2018-12-12T10:10:35Z date_updated: 2020-07-14T12:45:00Z file_id: '4823' file_name: IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf file_size: 577415 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 69' issue: '5' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 1101 - 1112 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Evolution publication_status: published publisher: Wiley publist_id: '5656' pubrep_id: '560' quality_controlled: '1' scopus_import: 1 status: public title: The interpretation of selection coefficients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2015' ... --- _id: '1525' abstract: - lang: eng text: 'Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.' article_processing_charge: No article_type: original author: - first_name: Bruno full_name: Bauer, Bruno last_name: Bauer - first_name: Guido full_name: Blechl, Guido last_name: Blechl - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Andreas full_name: Ferus, Andreas last_name: Ferus - first_name: Anton full_name: Graschopf, Anton last_name: Graschopf - first_name: Thomas full_name: König, Thomas last_name: König - first_name: Katja full_name: Mayer, Katja last_name: Mayer - first_name: Falk full_name: Reckling, Falk last_name: Reckling - first_name: Katharina full_name: Rieck, Katharina last_name: Rieck - first_name: Peter full_name: Seitz, Peter last_name: Seitz - first_name: Herwig full_name: Stöger, Herwig last_name: Stöger - first_name: Elvira full_name: Welzig, Elvira last_name: Welzig citation: ama: Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178 apa: Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. Verein Österreichischer Bibliothekare. https://doi.org/10.5281/zenodo.33178 chicago: Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen. Verein Österreichischer Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178. ieee: B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015. ista: Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607. mla: Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178. short: B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen 68 (2015) 580–607. date_created: 2018-12-11T11:52:31Z date_published: 2015-11-12T00:00:00Z date_updated: 2021-01-12T06:51:22Z day: '12' ddc: - '020' department: - _id: E-Lib doi: 10.5281/zenodo.33178 file: - access_level: open_access checksum: a495fe253bbc7615b1d60e9e85c94408 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:59Z date_updated: 2020-07-14T12:45:00Z file_id: '5317' file_name: IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf file_size: 931707 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 68' issue: '3' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 580 - 607 publication: VÖB Mitteilungen publication_status: published publisher: Verein Österreichischer Bibliothekare publist_id: '5648' pubrep_id: '720' quality_controlled: '1' scopus_import: 1 status: public title: Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA 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: 68 year: '2015' ... --- _id: '1520' abstract: - lang: eng text: Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs. author: - first_name: Gaurav full_name: Bharaj, Gaurav last_name: Bharaj - first_name: Stelian full_name: Coros, Stelian last_name: Coros - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: James full_name: Tompkin, James last_name: Tompkin - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister citation: ama: 'Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:10.1145/2786784.2786803' apa: 'Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., & Pfister, H. (2015). Computational design of walking automata (pp. 93–100). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2786784.2786803' chicago: Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. https://doi.org/10.1145/2786784.2786803. ieee: 'G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister, “Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100.' ista: 'Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015. Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 93–100.' mla: Bharaj, Gaurav, et al. Computational Design of Walking Automata. ACM, 2015, pp. 93–100, doi:10.1145/2786784.2786803. short: G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100. conference: end_date: 2015-08-09 location: Los Angeles, CA, United States name: 'SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation' start_date: 2015-08-07 date_created: 2018-12-11T11:52:30Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:21Z day: '01' department: - _id: BeBi doi: 10.1145/2786784.2786803 language: - iso: eng month: '08' oa_version: None page: 93 - 100 publication_identifier: isbn: - 978-1-4503-3496-9 publication_status: published publisher: ACM publist_id: '5655' quality_controlled: '1' scopus_import: 1 status: public title: Computational design of walking automata type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1532' abstract: - lang: eng text: Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels. article_processing_charge: No article_type: original author: - first_name: Huaiyu full_name: Yang, Huaiyu last_name: Yang - first_name: Jenny full_name: Von Der Fecht Bartenbach, Jenny last_name: Von Der Fecht Bartenbach - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Lohmann, Jan last_name: Lohmann - first_name: Benjamin full_name: Neuhäuser, Benjamin last_name: Neuhäuser - first_name: Uwe full_name: Ludewig, Uwe last_name: Ludewig citation: ama: Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251. doi:10.1071/FP14171 apa: Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. CSIRO. https://doi.org/10.1071/FP14171 chicago: Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171. ieee: H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology, vol. 42, no. 3. CSIRO, pp. 239–251, 2015. ista: Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251. mla: Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171. short: H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251. date_created: 2018-12-11T11:52:34Z date_published: 2015-03-01T00:00:00Z date_updated: 2022-05-24T09:02:24Z day: '01' department: - _id: JiFr doi: 10.1071/FP14171 external_id: pmid: - '32480670' intvolume: ' 42' issue: '3' language: - iso: eng month: '03' oa_version: None page: 239 - 251 pmid: 1 publication: Functional Plant Biology publication_identifier: issn: - 1445-4408 publication_status: published publisher: CSIRO publist_id: '5639' quality_controlled: '1' scopus_import: '1' status: public title: Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2015' ... --- _id: '1531' abstract: - lang: eng text: The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece. alternative_title: - Mathematics and Visualization article_processing_charge: No author: - first_name: Valentin full_name: Zobel, Valentin last_name: Zobel - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Ingrid full_name: Hotz, Ingrid last_name: Hotz citation: ama: 'Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Vol 40. 1st ed. Springer; 2015:257-267. doi:10.1007/978-3-319-15090-1_13' apa: Zobel, V., Reininghaus, J., & Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz & T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data (1st ed., Vol. 40, pp. 257–267). Springer. https://doi.org/10.1007/978-3-319-15090-1_13 chicago: Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. https://doi.org/10.1007/978-3-319-15090-1_13. ieee: V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267. ista: 'Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267.' mla: Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:10.1007/978-3-319-15090-1_13. short: V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267. date_created: 2018-12-11T11:52:33Z date_published: 2015-01-01T00:00:00Z date_updated: 2022-06-10T09:50:14Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-319-15090-1_13 edition: '1' editor: - first_name: Ingrid full_name: Hotz, Ingrid last_name: Hotz - first_name: Thomas full_name: Schultz, Thomas last_name: Schultz intvolume: ' 40' language: - iso: eng month: '01' oa_version: None page: 257 - 267 publication: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data publication_identifier: isbn: - 978-3-319-15089-5 publication_status: published publisher: Springer publist_id: '5640' quality_controlled: '1' scopus_import: '1' status: public title: Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2015' ... --- _id: '1530' abstract: - lang: eng text: In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle. article_number: '066003' author: - first_name: Veronika full_name: Bierbaum, Veronika id: 3FD04378-F248-11E8-B48F-1D18A9856A87 last_name: Bierbaum - first_name: Stefan full_name: Klumpp, Stefan last_name: Klumpp citation: ama: Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. Physical Biology. 2015;12(6). doi:10.1088/1478-3975/12/6/066003 apa: Bierbaum, V., & Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/12/6/066003 chicago: Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1478-3975/12/6/066003. ieee: V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” Physical Biology, vol. 12, no. 6. IOP Publishing Ltd., 2015. ista: Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003. mla: Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” Physical Biology, vol. 12, no. 6, 066003, IOP Publishing Ltd., 2015, doi:10.1088/1478-3975/12/6/066003. short: V. Bierbaum, S. Klumpp, Physical Biology 12 (2015). date_created: 2018-12-11T11:52:33Z date_published: 2015-09-25T00:00:00Z date_updated: 2021-01-12T06:51:25Z day: '25' department: - _id: MiSi doi: 10.1088/1478-3975/12/6/066003 intvolume: ' 12' issue: '6' language: - iso: eng month: '09' oa_version: None publication: Physical Biology publication_status: published publisher: IOP Publishing Ltd. publist_id: '5641' quality_controlled: '1' scopus_import: 1 status: public title: Impact of the cell division cycle on gene circuits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2015' ... --- _id: '1539' abstract: - lang: eng text: 'Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ' article_number: '244103' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 citation: ama: Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937 apa: Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937 chicago: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937. ieee: J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015. ista: Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103. mla: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937. short: J. Ruess, Journal of Chemical Physics 143 (2015). date_created: 2018-12-11T11:52:36Z date_published: 2015-12-22T00:00:00Z date_updated: 2021-01-12T06:51:28Z day: '22' ddc: - '000' department: - _id: ToHe - _id: GaTk doi: 10.1063/1.4937937 ec_funded: 1 file: - access_level: open_access checksum: 838657118ae286463a2b7737319f35ce content_type: application/pdf creator: system date_created: 2018-12-12T10:07:43Z date_updated: 2020-07-14T12:45:01Z file_id: '4641' file_name: IST-2016-593-v1+1_Minimal_moment_equations.pdf file_size: 605355 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 143' issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Chemical Physics publication_status: published publisher: American Institute of Physics publist_id: '5632' pubrep_id: '593' quality_controlled: '1' scopus_import: 1 status: public title: Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 143 year: '2015' ... --- _id: '1534' abstract: - lang: eng text: PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity. article_number: '8822' author: - first_name: Hongzhe full_name: Wang, Hongzhe last_name: Wang - first_name: Kezhen full_name: Yang, Kezhen last_name: Yang - first_name: Junjie full_name: Zou, Junjie last_name: Zou - first_name: Lingling full_name: Zhu, Lingling last_name: Zhu - first_name: Zidian full_name: Xie, Zidian last_name: Xie - first_name: Miyoterao full_name: Morita, Miyoterao last_name: Morita - first_name: Masao full_name: Tasaka, Masao last_name: Tasaka - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Erich full_name: Grotewold, Erich last_name: Grotewold - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Fred full_name: Sack, Fred last_name: Sack - first_name: Jie full_name: Le, Jie last_name: Le citation: ama: Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822 apa: Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822 chicago: Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822. ieee: H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822. mla: Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822. short: H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:34Z date_published: 2015-11-18T00:00:00Z date_updated: 2021-01-12T06:51:26Z day: '18' ddc: - '570' department: - _id: JiFr doi: 10.1038/ncomms9822 ec_funded: 1 file: - access_level: open_access checksum: 3c06735fc7cd7e482ca830cbd26001bf content_type: application/pdf creator: system date_created: 2018-12-12T10:17:07Z date_updated: 2020-07-14T12:45:01Z file_id: '5259' file_name: IST-2016-485-v1+1_ncomms9822.pdf file_size: 1852268 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5637' pubrep_id: '485' quality_controlled: '1' scopus_import: 1 status: public title: Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism 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: 6 year: '2015' ... --- _id: '1538' abstract: - lang: eng text: Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time. acknowledgement: 'J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Francesca full_name: Parise, Francesca last_name: Parise - first_name: Andreas full_name: Milias Argeitis, Andreas last_name: Milias Argeitis - first_name: Mustafa full_name: Khammash, Mustafa last_name: Khammash - first_name: John full_name: Lygeros, John last_name: Lygeros citation: ama: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112 apa: Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112 chicago: Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423947112. ieee: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015. ista: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153. mla: Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112. short: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153. date_created: 2018-12-11T11:52:36Z date_published: 2015-06-30T00:00:00Z date_updated: 2021-01-12T06:51:27Z day: '30' department: - _id: ToHe - _id: GaTk doi: 10.1073/pnas.1423947112 ec_funded: 1 external_id: pmid: - '26085136' intvolume: ' 112' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/ month: '06' oa: 1 oa_version: Submitted Version page: 8148 - 8153 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5633' quality_controlled: '1' scopus_import: 1 status: public title: Iterative experiment design guides the characterization of a light-inducible gene expression circuit type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1535' abstract: - lang: eng text: Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress. acknowledgement: This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino. article_processing_charge: No article_type: original author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Andrea full_name: Marcantoni, Andrea last_name: Marcantoni - first_name: Emilio full_name: Carbone, Emilio last_name: Carbone citation: ama: Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 2015;8(2):149-161. doi:10.2174/1874467208666150507105443 apa: Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443 chicago: Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015. https://doi.org/10.2174/1874467208666150507105443. ieee: D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” Current Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015. ista: Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161. mla: Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443. short: D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161. date_created: 2018-12-11T11:52:35Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:51:26Z day: '01' department: - _id: PeJo doi: 10.2174/1874467208666150507105443 external_id: pmid: - '25966692' intvolume: ' 8' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/ month: '10' oa: 1 oa_version: Submitted Version page: 149 - 161 pmid: 1 publication: Current Molecular Pharmacology publication_status: published publisher: Bentham Science Publishers publist_id: '5636' quality_controlled: '1' scopus_import: 1 status: public title: Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2015' ... --- _id: '1536' abstract: - lang: eng text: Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil. acknowledgement: "This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification." author: - first_name: Joëlle full_name: Sasse, Joëlle last_name: Sasse - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Christian full_name: Gübeli, Christian last_name: Gübeli - first_name: Guowei full_name: Liu, Guowei last_name: Liu - first_name: Xi full_name: Cheng, Xi last_name: Cheng - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Harro full_name: Bouwmeester, Harro last_name: Bouwmeester - first_name: Enrico full_name: Martinoia, Enrico last_name: Martinoia - first_name: Lorenzo full_name: Borghi, Lorenzo last_name: Borghi citation: ama: Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015 apa: Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015 chicago: Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015. ieee: J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” Current Biology, vol. 25, no. 5. Cell Press, pp. 647–655, 2015. ista: Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655. mla: Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015. short: J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655. date_created: 2018-12-11T11:52:35Z date_published: 2015-02-12T00:00:00Z date_updated: 2021-01-12T06:51:27Z day: '12' department: - _id: JiFr doi: 10.1016/j.cub.2015.01.015 intvolume: ' 25' issue: '5' language: - iso: eng month: '02' oa_version: None page: 647 - 655 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5635' quality_controlled: '1' scopus_import: 1 status: public title: Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '1533' abstract: - lang: eng text: This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts. author: - first_name: Wei full_name: Xia, Wei last_name: Xia - first_name: Csaba full_name: Domokos, Csaba id: 492DACF8-F248-11E8-B48F-1D18A9856A87 last_name: Domokos - first_name: Junjun full_name: Xiong, Junjun last_name: Xiong - first_name: Loongfah full_name: Cheong, Loongfah last_name: Cheong - first_name: Shuicheng full_name: Yan, Shuicheng last_name: Yan citation: ama: Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 2015;25(8):1295-1308. doi:10.1109/TCSVT.2014.2379972 apa: Xia, W., Domokos, C., Xiong, J., Cheong, L., & Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. IEEE. https://doi.org/10.1109/TCSVT.2014.2379972 chicago: Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology. IEEE, 2015. https://doi.org/10.1109/TCSVT.2014.2379972. ieee: W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015. ista: Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308. mla: Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” IEEE Transactions on Circuits and Systems for Video Technology, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:10.1109/TCSVT.2014.2379972. short: W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308. date_created: 2018-12-11T11:52:34Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:26Z day: '01' department: - _id: ChLa doi: 10.1109/TCSVT.2014.2379972 intvolume: ' 25' issue: '8' language: - iso: eng month: '08' oa_version: None page: 1295 - 1308 publication: IEEE Transactions on Circuits and Systems for Video Technology publication_status: published publisher: IEEE publist_id: '5638' quality_controlled: '1' scopus_import: 1 status: public title: Segmentation over detection via optimal sparse reconstructions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '1542' abstract: - lang: eng text: 'The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ' author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Golnaz full_name: Badkobeh, Golnaz last_name: Badkobeh - 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: Doğan full_name: Çörüş, Doğan last_name: Çörüş - first_name: Duccuong full_name: Dang, Duccuong last_name: Dang - first_name: Tobias full_name: Friedrich, Tobias last_name: Friedrich - first_name: Per full_name: Lehre, Per last_name: Lehre - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Andrew full_name: Sutton, Andrew last_name: Sutton - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011 apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011 chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011. ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015. ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43. mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011. short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43. date_created: 2018-12-11T11:52:37Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T06:51:29Z day: '21' ddc: - '570' department: - _id: NiBa - _id: CaGu doi: 10.1016/j.jtbi.2015.07.011 ec_funded: 1 file: - access_level: open_access checksum: 33b60ecfea60764756a9ee9df5eb65ca content_type: application/pdf creator: system date_created: 2018-12-12T10:16:53Z date_updated: 2020-07-14T12:45:01Z file_id: '5244' file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf file_size: 595307 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 383' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version page: 28 - 43 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: ' Journal of Theoretical Biology' publication_status: published publisher: Elsevier publist_id: '5629' pubrep_id: '483' quality_controlled: '1' scopus_import: 1 status: public title: Toward a unifying framework for evolutionary processes 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: 383 year: '2015' ... --- _id: '1546' abstract: - lang: eng text: Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (<30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This "perimeter release model" provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course. acknowledgement: This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS. author: - first_name: Yukihiro full_name: Nakamura, Yukihiro last_name: Nakamura - first_name: Harumi full_name: Harada, Harumi id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87 last_name: Harada orcid: 0000-0001-7429-7896 - first_name: Naomi full_name: Kamasawa, Naomi last_name: Kamasawa - first_name: Ko full_name: Matsui, Ko last_name: Matsui - first_name: Jason full_name: Rothman, Jason last_name: Rothman - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: R Angus full_name: Silver, R Angus last_name: Silver - first_name: David full_name: Digregorio, David last_name: Digregorio - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019 apa: Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.11.019 chicago: Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019. ieee: Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” Neuron, vol. 85, no. 1. Elsevier, pp. 145–158, 2015. ista: Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158. mla: Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019. short: Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158. date_created: 2018-12-11T11:52:39Z date_published: 2015-01-07T00:00:00Z date_updated: 2021-01-12T06:51:31Z day: '07' ddc: - '570' department: - _id: RySh doi: 10.1016/j.neuron.2014.11.019 file: - access_level: open_access checksum: 725f4d5be2dbb44b283ce722645ef37d content_type: application/pdf creator: system date_created: 2018-12-12T10:15:47Z date_updated: 2020-07-14T12:45:01Z file_id: '5170' file_name: IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf file_size: 3080111 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 85' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 145 - 158 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5625' pubrep_id: '482' quality_controlled: '1' scopus_import: 1 status: public title: Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development 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: 85 year: '2015' ... --- _id: '1541' abstract: - lang: eng text: We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision. acknowledgement: This work was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). alternative_title: - LNCS author: - first_name: Rajarshi full_name: Ray, Rajarshi last_name: Ray - first_name: Amit full_name: Gurung, Amit last_name: Gurung - first_name: Binayak full_name: Das, Binayak last_name: Das - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating reachability analysis on multi-core processors. 2015;9434:3-18. doi:10.1007/978-3-319-26287-1_1' apa: 'Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., & Grosu, R. (2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_1' chicago: 'Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov, and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_1.' ieee: 'R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed: Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer, pp. 3–18, 2015.' ista: 'Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating reachability analysis on multi-core processors. 9434, 3–18.' mla: 'Ray, Rajarshi, et al. XSpeed: Accelerating Reachability Analysis on Multi-Core Processors. Vol. 9434, Springer, 2015, pp. 3–18, doi:10.1007/978-3-319-26287-1_1.' short: R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18. conference: end_date: 2015-11-19 location: Haifa, Israel name: 'HVC: Haifa Verification Conference' start_date: 2015-11-17 date_created: 2018-12-11T11:52:37Z date_published: 2015-11-28T00:00:00Z date_updated: 2020-08-11T10:09:17Z day: '28' department: - _id: ToHe doi: 10.1007/978-3-319-26287-1_1 ec_funded: 1 intvolume: ' 9434' language: - iso: eng month: '11' oa_version: None page: 3 - 18 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '5630' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: 'XSpeed: Accelerating reachability analysis on multi-core processors' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9434 year: '2015' ... --- _id: '1543' abstract: - lang: eng text: A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta. author: - first_name: Yadira full_name: Olvera Carrillo, Yadira last_name: Olvera Carrillo - first_name: Michiel full_name: Van Bel, Michiel last_name: Van Bel - first_name: Tom full_name: Van Hautegem, Tom last_name: Van Hautegem - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Marlies full_name: Huysmans, Marlies last_name: Huysmans - first_name: Mária full_name: Šimášková, Mária last_name: Šimášková - first_name: Matthias full_name: Van Durme, Matthias last_name: Van Durme - first_name: Pierre full_name: Buscaill, Pierre last_name: Buscaill - first_name: Susana full_name: Rivas, Susana last_name: Rivas - first_name: Núria full_name: Coll, Núria last_name: Coll - first_name: Frederik full_name: Coppens, Frederik last_name: Coppens - first_name: Steven full_name: Maere, Steven last_name: Maere - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack citation: ama: Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699. doi:10.1104/pp.15.00769 apa: Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.15.00769 chicago: Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology. American Society of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769. ieee: Y. Olvera Carrillo et al., “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015. ista: Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699. mla: Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769. short: Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699. date_created: 2018-12-11T11:52:38Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:30Z day: '01' department: - _id: JiFr doi: 10.1104/pp.15.00769 intvolume: ' 169' issue: '4' language: - iso: eng month: '12' oa_version: None page: 2684 - 2699 publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '5628' scopus_import: 1 status: public title: A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 169 year: '2015' ... --- _id: '1544' abstract: - lang: eng text: 'Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.' author: - first_name: Phuong full_name: Nguyen, Phuong last_name: Nguyen - first_name: Christine full_name: Field, Christine last_name: Field - first_name: Aaron full_name: Groen, Aaron last_name: Groen - first_name: Timothy full_name: Mitchison, Timothy last_name: Mitchison - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007' apa: Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241). Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007 chicago: Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007. ieee: P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in Building a Cell from its Components Parts, vol. 128, Academic Press, 2015, pp. 223–241. ista: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.' mla: Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” Building a Cell from Its Components Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007. short: P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241. date_created: 2018-12-11T11:52:38Z date_published: 2015-04-08T00:00:00Z date_updated: 2021-01-12T06:51:30Z day: '08' department: - _id: MaLo doi: 10.1016/bs.mcb.2015.01.007 external_id: pmid: - '25997350' intvolume: ' 128' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/ month: '04' oa: 1 oa_version: Submitted Version page: 223 - 241 pmid: 1 publication: Building a Cell from its Components Parts publication_status: published publisher: Academic Press publist_id: '5627' quality_controlled: '1' scopus_import: 1 status: public title: Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2015' ... --- _id: '1540' abstract: - lang: eng text: 'Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants'' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.' acknowledgement: 'The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.' author: - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Lucie full_name: Crhák Khaitová, Lucie last_name: Crhák Khaitová - first_name: Souad full_name: Mroue, Souad last_name: Mroue - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256 apa: Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv256 chicago: Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv256. ieee: H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015. ista: Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042. mla: Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256. short: H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042. date_created: 2018-12-11T11:52:36Z date_published: 2015-05-05T00:00:00Z date_updated: 2021-01-12T06:51:29Z day: '05' department: - _id: EvBe doi: 10.1093/jxb/erv256 intvolume: ' 66' issue: '16' language: - iso: eng month: '05' oa_version: None page: 5029 - 5042 publication: Journal of Experimental Botany publication_status: published publisher: Oxford University Press publist_id: '5631' quality_controlled: '1' scopus_import: 1 status: public title: The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2015' ... --- _id: '1551' abstract: - lang: eng text: 'Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen''s genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.' acknowledgement: We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM. author: - first_name: Leila full_name: El Masri, Leila id: 349A6E66-F248-11E8-B48F-1D18A9856A87 last_name: El Masri - first_name: Antoine full_name: Branca, Antoine last_name: Branca - first_name: Anna full_name: Sheppard, Anna last_name: Sheppard - first_name: Andrei full_name: Papkou, Andrei last_name: Papkou - first_name: David full_name: Laehnemann, David last_name: Laehnemann - first_name: Patrick full_name: Guenther, Patrick last_name: Guenther - first_name: Swantje full_name: Prahl, Swantje last_name: Prahl - first_name: Manja full_name: Saebelfeld, Manja last_name: Saebelfeld - first_name: Jacqueline full_name: Hollensteiner, Jacqueline last_name: Hollensteiner - first_name: Heiko full_name: Liesegang, Heiko last_name: Liesegang - first_name: Elzbieta full_name: Brzuszkiewicz, Elzbieta last_name: Brzuszkiewicz - first_name: Rolf full_name: Daniel, Rolf last_name: Daniel - first_name: Nico full_name: Michiels, Nico last_name: Michiels - first_name: Rebecca full_name: Schulte, Rebecca last_name: Schulte - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Arndt full_name: Telschow, Arndt last_name: Telschow - first_name: Erich full_name: Bornberg Bauer, Erich last_name: Bornberg Bauer - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg citation: ama: 'El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169' apa: 'El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169' chicago: 'El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.' ieee: 'L. El Masri et al., “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.' ista: 'El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.' mla: 'El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.' short: L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30. date_created: 2018-12-11T11:52:40Z date_published: 2015-06-04T00:00:00Z date_updated: 2021-01-12T06:51:33Z day: '04' ddc: - '570' department: - _id: SyCr doi: 10.1371/journal.pbio.1002169 ec_funded: 1 file: - access_level: open_access checksum: 30dee7a2c11ed09f2f5634655c0146f8 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:13Z date_updated: 2020-07-14T12:45:02Z file_id: '5063' file_name: IST-2016-481-v1+1_journal.pbio.1002169.pdf file_size: 3468956 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 13' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1 - 30 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '5620' pubrep_id: '481' quality_controlled: '1' scopus_import: 1 status: public title: 'Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2015' ... --- _id: '1549' abstract: - lang: eng text: Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology. author: - first_name: Catherine full_name: Mckenzie, Catherine id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87 last_name: Mckenzie - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: Novel Chemical Tools to Study Ion Channel Biology. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:10.1007/978-1-4939-2845-3_6' apa: 'Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In Novel chemical tools to study ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6' chicago: 'Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.' ieee: 'C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in Novel chemical tools to study ion channel biology, vol. 869, Springer, 2015, pp. 101–117.' ista: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.' mla: 'Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol. 869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.' short: C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117. date_created: 2018-12-11T11:52:39Z date_published: 2015-09-18T00:00:00Z date_updated: 2021-01-12T06:51:32Z day: '18' ddc: - '571' - '576' department: - _id: HaJa doi: 10.1007/978-1-4939-2845-3_6 file: - access_level: open_access checksum: bd1bfdf2423a0c3b6e7cabfa8b44bc0f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:02Z date_updated: 2020-07-14T12:45:01Z file_id: '4854' file_name: IST-2017-839-v1+1_mckenzie.pdf file_size: 1919655 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 869' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 101 - 117 publication: Novel chemical tools to study ion channel biology publication_identifier: isbn: - 978-1-4939-2844-6 publication_status: published publisher: Springer publist_id: '5622' pubrep_id: '839' quality_controlled: '1' scopus_import: 1 series_title: Advances in Experimental Medicine and Biology status: public title: 'Flipping the photoswitch: Ion channels under light control' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 869 year: '2015' ... --- _id: '1548' abstract: - lang: eng text: Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen. author: - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Christina full_name: Höfling, Christina last_name: Höfling - first_name: Momir full_name: Futo, Momir last_name: Futo - first_name: Jörn full_name: Scharsack, Jörn last_name: Scharsack - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15' apa: 'Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. American Society for Microbiology. https://doi.org/10.1128/AEM.02051-15' chicago: 'Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology. American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.' ieee: 'B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” Applied and Environmental Microbiology, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.' ista: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.' mla: 'Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:10.1128/AEM.02051-15.' short: B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144. date_created: 2018-12-11T11:52:39Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:31Z day: '01' department: - _id: SyCr doi: 10.1128/AEM.02051-15 external_id: pmid: - '26386058' intvolume: ' 81' issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/ month: '12' oa: 1 oa_version: Submitted Version page: 8135 - 8144 pmid: 1 publication: Applied and Environmental Microbiology publication_status: published publisher: American Society for Microbiology publist_id: '5623' quality_controlled: '1' scopus_import: 1 status: public title: 'Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2015' ... --- _id: '1553' abstract: - lang: eng text: Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns. author: - first_name: Paolo full_name: Maiuri, Paolo last_name: Maiuri - first_name: Jean full_name: Rupprecht, Jean last_name: Rupprecht - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Olivier full_name: Bénichou, Olivier last_name: Bénichou - first_name: Nicolas full_name: Carpi, Nicolas last_name: Carpi - first_name: Mathieu full_name: Coppey, Mathieu last_name: Coppey - first_name: Simon full_name: De Beco, Simon last_name: De Beco - first_name: Nir full_name: Gov, Nir last_name: Gov - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Carolina full_name: Lage Crespo, Carolina last_name: Lage Crespo - first_name: Franziska full_name: Lautenschlaeger, Franziska last_name: Lautenschlaeger - first_name: Maël full_name: Le Berre, Maël last_name: Le Berre - first_name: Ana full_name: Lennon Duménil, Ana last_name: Lennon Duménil - first_name: Matthew full_name: Raab, Matthew last_name: Raab - first_name: Hawa full_name: Thiam, Hawa last_name: Thiam - first_name: Matthieu full_name: Piel, Matthieu last_name: Piel - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez citation: ama: Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 2015;161(2):374-386. doi:10.1016/j.cell.2015.01.056 apa: Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N., … Voituriez, R. (2015). Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.056 chicago: Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.056. ieee: P. Maiuri et al., “Actin flows mediate a universal coupling between cell speed and cell persistence,” Cell, vol. 161, no. 2. Cell Press, pp. 374–386, 2015. ista: Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 161(2), 374–386. mla: Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” Cell, vol. 161, no. 2, Cell Press, 2015, pp. 374–86, doi:10.1016/j.cell.2015.01.056. short: P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M. Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger, M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez, Cell 161 (2015) 374–386. date_created: 2018-12-11T11:52:41Z date_published: 2015-04-09T00:00:00Z date_updated: 2021-01-12T06:51:33Z day: '09' department: - _id: MiSi - _id: CaHe doi: 10.1016/j.cell.2015.01.056 ec_funded: 1 intvolume: ' 161' issue: '2' language: - iso: eng month: '04' oa_version: None page: 374 - 386 project: - _id: 2529486C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T 560-B17 name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) - _id: 25ABD200-B435-11E9-9278-68D0E5697425 grant_number: RGP0058/2011 name: 'Cell migration in complex environments: from in vivo experiments to theoretical models' publication: Cell publication_status: published publisher: Cell Press publist_id: '5618' quality_controlled: '1' scopus_import: 1 status: public title: Actin flows mediate a universal coupling between cell speed and cell persistence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 161 year: '2015' ... --- _id: '1550' abstract: - lang: eng text: The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute. acknowledgement: "Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n" author: - first_name: Christian full_name: Mayer, Christian last_name: Mayer - first_name: Xavier full_name: Jaglin, Xavier last_name: Jaglin - first_name: Lucy full_name: Cobbs, Lucy last_name: Cobbs - first_name: Rachel full_name: Bandler, Rachel last_name: Bandler - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Constance full_name: Cepko, Constance last_name: Cepko - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Gord full_name: Fishell, Gord last_name: Fishell citation: ama: Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011 apa: Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011 chicago: Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011. ieee: C. Mayer et al., “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” Neuron, vol. 87, no. 5. Elsevier, pp. 989–998, 2015. ista: Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998. mla: Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011. short: C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998. date_created: 2018-12-11T11:52:40Z date_published: 2015-09-02T00:00:00Z date_updated: 2021-01-12T06:51:32Z day: '02' department: - _id: SiHi doi: 10.1016/j.neuron.2015.07.011 external_id: pmid: - '26299473' intvolume: ' 87' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/ month: '09' oa: 1 oa_version: Submitted Version page: 989 - 998 pmid: 1 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5621' quality_controlled: '1' scopus_import: 1 status: public title: Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2015' ... --- _id: '1547' abstract: - lang: eng text: Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice. author: - first_name: Fatemeh full_name: Mohammadi, Fatemeh id: 2C29581E-F248-11E8-B48F-1D18A9856A87 last_name: Mohammadi - first_name: Somayeh full_name: Moradi, Somayeh last_name: Moradi citation: ama: Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977 apa: Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. Korean Mathematical Society. https://doi.org/10.4134/BKMS.2015.52.3.977 chicago: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977. ieee: F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015. ista: Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986. mla: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977. short: F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986. date_created: 2018-12-11T11:52:39Z date_published: 2015-05-31T00:00:00Z date_updated: 2021-01-12T06:51:31Z day: '31' department: - _id: CaUh doi: 10.4134/BKMS.2015.52.3.977 intvolume: ' 52' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/0901.3015 month: '05' oa: 1 oa_version: Preprint page: 977 - 986 publication: Bulletin of the Korean Mathematical Society publication_identifier: eissn: - 2234-3016 publication_status: published publisher: Korean Mathematical Society publist_id: '5624' quality_controlled: '1' scopus_import: 1 status: public title: Resolution of unmixed bipartite graphs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2015' ... --- _id: '1556' abstract: - lang: eng text: The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators. author: - first_name: Yuebin full_name: Jia, Yuebin last_name: Jia - first_name: Huiyu full_name: Tian, Huiyu last_name: Tian - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Qianqian full_name: Yu, Qianqian last_name: Yu - first_name: Lei full_name: Wang, Lei last_name: Wang - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding citation: ama: Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230 apa: Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230 chicago: Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230. ieee: Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015. ista: Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642. mla: Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230. short: Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642. date_created: 2018-12-11T11:52:42Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:35Z day: '01' ddc: - '570' department: - _id: JiFr doi: 10.1093/jxb/erv230 file: - access_level: open_access checksum: 257919be0ce3d306185d3891ad7acf39 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:02Z date_updated: 2020-07-14T12:45:02Z file_id: '5051' file_name: IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf file_size: 7753043 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 66' issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 4631 - 4642 publication: Journal of Experimental Botany publication_status: published publisher: Oxford University Press publist_id: '5615' pubrep_id: '480' quality_controlled: '1' scopus_import: 1 status: public title: The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development 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: 66 year: '2015' ... --- _id: '1555' abstract: - lang: eng text: We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations. acknowledgement: Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project. article_processing_charge: No article_type: original author: - first_name: Diána full_name: Knipl, Diána last_name: Knipl - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk - first_name: Gergely full_name: Röst, Gergely last_name: Röst citation: ama: Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017. doi:10.1137/140993934 apa: Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934 chicago: Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934. ieee: D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015. ista: Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017. mla: Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934. short: D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017. date_created: 2018-12-11T11:52:42Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:51:34Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1137/140993934 ec_funded: 1 intvolume: ' 14' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://discovery.ucl.ac.uk/1473750/1/99393.pdf month: '01' oa: 1 oa_version: Published Version page: 980 - 1017 project: - _id: 255F06BE-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '622033' name: Persistent Homology - Images, Data and Maps publication: SIAM Journal on Applied Dynamical Systems publication_identifier: eissn: - 1536-0040 publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '5616' quality_controlled: '1' scopus_import: 1 status: public title: Rich bifurcation structure in a two patch vaccination model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2015' ... --- _id: '1558' abstract: - lang: eng text: CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation. author: - first_name: Maria full_name: Ivanchenko, Maria last_name: Ivanchenko - first_name: Jinsheng full_name: Zhu, Jinsheng last_name: Zhu - first_name: Bangjun full_name: Wang, Bangjun last_name: Wang - first_name: Eva full_name: Medvecka, Eva id: 298814E2-F248-11E8-B48F-1D18A9856A87 last_name: Medvecka - first_name: Yunlong full_name: Du, Yunlong last_name: Du - first_name: Elisa full_name: Azzarello, Elisa last_name: Azzarello - first_name: Stefano full_name: Mancuso, Stefano last_name: Mancuso - first_name: Molly full_name: Megraw, Molly last_name: Megraw - first_name: Sergei full_name: Filichkin, Sergei last_name: Filichkin - first_name: Joseph full_name: Dubrovsky, Joseph last_name: Dubrovsky - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Markus full_name: Geisler, Markus last_name: Geisler citation: ama: Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 2015;142(4):712-721. doi:10.1242/dev.113225 apa: Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. Company of Biologists. https://doi.org/10.1242/dev.113225 chicago: Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225. ieee: M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” Development, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015. ista: Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721. mla: Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225. short: M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721. date_created: 2018-12-11T11:52:42Z date_published: 2015-02-15T00:00:00Z date_updated: 2021-01-12T06:51:35Z day: '15' department: - _id: JiFr doi: 10.1242/dev.113225 intvolume: ' 142' issue: '4' language: - iso: eng month: '02' oa_version: None page: 712 - 721 publication: Development publication_status: published publisher: Company of Biologists publist_id: '5613' quality_controlled: '1' scopus_import: 1 status: public title: The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 142 year: '2015' ... --- _id: '1557' abstract: - lang: eng text: γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons. acknowledgement: "Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology" author: - first_name: Fariba full_name: Javdani, Fariba last_name: Javdani - first_name: Krisztina full_name: Holló, Krisztina last_name: Holló - first_name: Krisztina full_name: Hegedűs, Krisztina last_name: Hegedűs - first_name: Gréta full_name: Kis, Gréta last_name: Kis - first_name: Zoltán full_name: Hegyi, Zoltán last_name: Hegyi - first_name: Klaudia full_name: Dócs, Klaudia last_name: Dócs - first_name: Yu full_name: Kasugai, Yu last_name: Kasugai - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Miklós full_name: Antal, Miklós last_name: Antal citation: ama: Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 2015;523(13):1967-1983. doi:10.1002/cne.23774 apa: Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23774 chicago: Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology. Wiley-Blackwell, 2015. https://doi.org/10.1002/cne.23774. ieee: F. Javdani et al., “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” Journal of Comparative Neurology, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015. ista: Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983. mla: Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” Journal of Comparative Neurology, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:10.1002/cne.23774. short: F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983. date_created: 2018-12-11T11:52:42Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:51:35Z day: '01' department: - _id: RySh doi: 10.1002/cne.23774 intvolume: ' 523' issue: '13' language: - iso: eng month: '09' oa_version: None page: 1967 - 1983 publication: Journal of Comparative Neurology publication_status: published publisher: Wiley-Blackwell publist_id: '5614' quality_controlled: '1' scopus_import: 1 status: public title: Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 523 year: '2015' ... --- _id: '1559' abstract: - lang: eng text: 'There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).' author: - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112 apa: Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511366112 chicago: Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112. ieee: R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015. ista: Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641. mla: Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:10.1073/pnas.1511366112. short: R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641. date_created: 2018-12-11T11:52:43Z date_published: 2015-12-22T00:00:00Z date_updated: 2021-01-12T06:51:36Z day: '22' department: - _id: KrCh doi: 10.1073/pnas.1511366112 external_id: pmid: - '26644569' intvolume: ' 112' issue: '51' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/ month: '12' oa: 1 oa_version: Submitted Version page: 15636 - 15641 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5612' quality_controlled: '1' scopus_import: 1 status: public title: Computational complexity of ecological and evolutionary spatial dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1561' abstract: - lang: eng text: Replication-deficient recombinant adenoviruses are potent vectors for the efficient transient expression of exogenous genes in resting immune cells. However, most leukocytes are refractory to efficient adenoviral transduction as they lack expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle, we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously, CARΔ1 expression permits selective and highly efficient adenoviral transduction of immune cell populations, such as mast cells or T cells, directly ex vivo in bulk cultures without prior cell purification or activation. Furthermore, we show that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function mouse strain will hence be a valuable tool to rapidly dissect the function of specific genes in leukocyte physiology. author: - first_name: Klaus full_name: Heger, Klaus last_name: Heger - first_name: Maike full_name: Kober, Maike last_name: Kober - first_name: David full_name: Rieß, David last_name: Rieß - first_name: Christoph full_name: Drees, Christoph last_name: Drees - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Arianna full_name: Bertossi, Arianna last_name: Bertossi - first_name: Axel full_name: Roers, Axel last_name: Roers - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Marc full_name: Schmidt Supprian, Marc last_name: Schmidt Supprian citation: ama: Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 2015;45(6):1614-1620. doi:10.1002/eji.201545457 apa: Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. Wiley. https://doi.org/10.1002/eji.201545457 chicago: Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries, Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology. Wiley, 2015. https://doi.org/10.1002/eji.201545457. ieee: K. Heger et al., “A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors,” European Journal of Immunology, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015. ista: Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK, Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 45(6), 1614–1620. mla: Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” European Journal of Immunology, vol. 45, no. 6, Wiley, 2015, pp. 1614–20, doi:10.1002/eji.201545457. short: K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers, M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620. date_created: 2018-12-11T11:52:44Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:51:36Z day: '01' department: - _id: MiSi doi: 10.1002/eji.201545457 intvolume: ' 45' issue: '6' language: - iso: eng month: '06' oa_version: None page: 1614 - 1620 publication: European Journal of Immunology publication_status: published publisher: Wiley publist_id: '5610' quality_controlled: '1' scopus_import: 1 status: public title: A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2015' ... --- _id: '1554' abstract: - lang: eng text: The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species. author: - first_name: Cheyang full_name: Liao, Cheyang last_name: Liao - first_name: Wouter full_name: Smet, Wouter last_name: Smet - first_name: Géraldine full_name: Brunoud, Géraldine last_name: Brunoud - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida - first_name: Teva full_name: Vernoux, Teva last_name: Vernoux - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279 apa: Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279 chicago: Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279. ieee: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015. ista: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210. mla: Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279. short: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210. date_created: 2018-12-11T11:52:41Z date_published: 2015-02-26T00:00:00Z date_updated: 2021-01-12T06:51:34Z day: '26' department: - _id: JiFr doi: 10.1038/nmeth.3279 external_id: pmid: - '25643149' intvolume: ' 12' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/ month: '02' oa: 1 oa_version: Submitted Version page: 207 - 210 pmid: 1 publication: Nature Methods publication_status: published publisher: Nature Publishing Group publist_id: '5617' quality_controlled: '1' scopus_import: 1 status: public title: Reporters for sensitive and quantitative measurement of auxin response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2015' ... --- _id: '1560' abstract: - lang: eng text: Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function. author: - first_name: Miroslav full_name: Hons, Miroslav id: 4167FE56-F248-11E8-B48F-1D18A9856A87 last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Hons M, Sixt MK. The lymph node filter revealed. Nature Immunology. 2015;16(4):338-340. doi:10.1038/ni.3126 apa: Hons, M., & Sixt, M. K. (2015). The lymph node filter revealed. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3126 chicago: Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” Nature Immunology. Nature Publishing Group, 2015. https://doi.org/10.1038/ni.3126. ieee: M. Hons and M. K. Sixt, “The lymph node filter revealed,” Nature Immunology, vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015. ista: Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology. 16(4), 338–340. mla: Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” Nature Immunology, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:10.1038/ni.3126. short: M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340. date_created: 2018-12-11T11:52:43Z date_published: 2015-03-19T00:00:00Z date_updated: 2021-01-12T06:51:36Z day: '19' department: - _id: MiSi doi: 10.1038/ni.3126 intvolume: ' 16' issue: '4' language: - iso: eng month: '03' oa_version: None page: 338 - 340 publication: Nature Immunology publication_status: published publisher: Nature Publishing Group publist_id: '5611' quality_controlled: '1' scopus_import: 1 status: public title: The lymph node filter revealed type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2015' ... --- _id: '1565' abstract: - lang: eng text: Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release. acknowledgement: "This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support." author: - first_name: Daniela full_name: Gavello, Daniela last_name: Gavello - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Sara full_name: Gosso, Sara last_name: Gosso - first_name: Emilio full_name: Carbone, Emilio last_name: Carbone - first_name: Valentina full_name: Carabelli, Valentina last_name: Carabelli citation: ama: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 2015;593(22):4835-4853. doi:10.1113/JP271078 apa: Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078 chicago: Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078. ieee: D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015. ista: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853. mla: Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:10.1113/JP271078. short: D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853. date_created: 2018-12-11T11:52:45Z date_published: 2015-11-15T00:00:00Z date_updated: 2021-01-12T06:51:38Z day: '15' department: - _id: PeJo doi: 10.1113/JP271078 external_id: pmid: - '26282459' intvolume: ' 593' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/ month: '11' oa: 1 oa_version: Submitted Version page: 4835 - 4853 pmid: 1 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '5606' quality_controlled: '1' scopus_import: 1 status: public title: Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 593 year: '2015' ... --- _id: '1562' abstract: - lang: eng text: The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor. acknowledgement: This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF]. article_type: original author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177 apa: Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv177 chicago: Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177. ieee: P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015. ista: Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065. mla: Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177. short: P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065. date_created: 2018-12-11T11:52:44Z date_published: 2015-08-01T00:00:00Z date_updated: 2023-02-23T10:04:26Z day: '01' department: - _id: JiFr - _id: EM-Fac doi: 10.1093/jxb/erv177 ec_funded: 1 intvolume: ' 66' issue: '16' language: - iso: eng month: '08' oa_version: None page: 5055 - 5065 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Journal of Experimental Botany publication_status: published publisher: Oxford University Press publist_id: '5609' quality_controlled: '1' scopus_import: 1 status: public title: Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2015' ... --- _id: '1564' article_number: '145' author: - first_name: Matthieu full_name: Gilson, Matthieu last_name: Gilson - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Friedemann full_name: Zenke, Friedemann last_name: Zenke citation: ama: 'Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145' apa: 'Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145' chicago: 'Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.' ieee: 'M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.' ista: 'Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.' mla: 'Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.' short: M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015). date_created: 2018-12-11T11:52:45Z date_published: 2015-11-30T00:00:00Z date_updated: 2021-01-12T06:51:37Z day: '30' ddc: - '570' department: - _id: GaTk doi: 10.3389/fncom.2015.00145 ec_funded: 1 file: - access_level: open_access checksum: cea73b6d3ef1579f32da10b82f4de4fd content_type: application/pdf creator: system date_created: 2018-12-12T10:12:09Z date_updated: 2020-07-14T12:45:02Z file_id: '4927' file_name: IST-2016-479-v1+1_fncom-09-00145.pdf file_size: 187038 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 9' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Frontiers in Computational Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '5607' pubrep_id: '479' quality_controlled: '1' scopus_import: 1 status: public title: 'Editorial: Emergent neural computation from the interaction of different forms of plasticity' 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: '2015' ... --- _id: '1568' abstract: - lang: eng text: Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions. acknowledgement: This research is supported by the project No. 477 of P.G. Demidov Yaroslavl State University within State Assignment for Research. author: - first_name: Olga full_name: Dunaeva, Olga last_name: Dunaeva - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Lukyanov, Anton last_name: Lukyanov - first_name: Michael full_name: Machin, Michael last_name: Machin - first_name: Daria full_name: Malkova, Daria last_name: Malkova citation: ama: 'Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification of endoscopy images with persistent homology. In: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. IEEE; 2015:7034731. doi:10.1109/SYNASC.2014.81' apa: 'Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., & Malkova, D. (2015). The classification of endoscopy images with persistent homology. In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (p. 7034731). Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC.2014.81' chicago: Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.” In Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, 7034731. IEEE, 2015. https://doi.org/10.1109/SYNASC.2014.81. ieee: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The classification of endoscopy images with persistent homology,” in Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, Timisoara, Romania, 2015, p. 7034731. ista: 'Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification of endoscopy images with persistent homology. Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symbolic and Numeric Algorithms for Scientific Computing, 7034731.' mla: Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731, doi:10.1109/SYNASC.2014.81. short: O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731. conference: end_date: 2014-09-25 location: Timisoara, Romania name: 'SYNASC: Symbolic and Numeric Algorithms for Scientific Computing' start_date: 2014-09-22 date_created: 2018-12-11T11:52:46Z date_published: 2015-02-05T00:00:00Z date_updated: 2023-02-21T16:57:29Z day: '05' department: - _id: HeEd doi: 10.1109/SYNASC.2014.81 language: - iso: eng month: '02' oa_version: None page: '7034731' publication: Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing publication_status: published publisher: IEEE publist_id: '5603' quality_controlled: '1' related_material: record: - id: '1289' relation: later_version status: public scopus_import: 1 status: public title: The classification of endoscopy images with persistent homology type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1567' abstract: - lang: eng text: My personal journey to the fascinating world of geometric forms started more than 30 years ago with the invention of alpha shapes in the plane. It took about 10 years before we generalized the concept to higher dimensions, we produced working software with a graphics interface for the three-dimensional case. At the same time, we added homology to the computations. Needless to say that this foreshadowed the inception of persistent homology, because it suggested the study of filtrations to capture the scale of a shape or data set. Importantly, this method has fast algorithms. The arguably most useful result on persistent homology is the stability of its diagrams under perturbations. alternative_title: - LNCS article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Edelsbrunner H. Shape, homology, persistence, and stability. In: 23rd International Symposium. Vol 9411. Springer Nature; 2015.' apa: 'Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In 23rd International Symposium (Vol. 9411). Los Angeles, CA, United States: Springer Nature.' chicago: Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In 23rd International Symposium, Vol. 9411. Springer Nature, 2015. ieee: H. Edelsbrunner, “Shape, homology, persistence, and stability,” in 23rd International Symposium, Los Angeles, CA, United States, 2015, vol. 9411. ista: 'Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411.' mla: Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” 23rd International Symposium, vol. 9411, Springer Nature, 2015. short: H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015. conference: end_date: 2015-09-26 location: Los Angeles, CA, United States name: 'GD: Graph Drawing and Network Visualization' start_date: 2015-09-24 date_created: 2018-12-11T11:52:46Z date_published: 2015-01-01T00:00:00Z date_updated: 2022-01-28T08:25:00Z day: '01' department: - _id: HeEd intvolume: ' 9411' language: - iso: eng month: '01' oa_version: None publication: 23rd International Symposium publication_status: published publisher: Springer Nature publist_id: '5604' quality_controlled: '1' scopus_import: '1' status: public title: Shape, homology, persistence, and stability type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9411 year: '2015' ... --- _id: '1563' abstract: - lang: eng text: For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\tt http://www.pawelpilarczyk.com/combtop/}. author: - first_name: Grzegorz full_name: Graff, Grzegorz last_name: Graff - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk citation: ama: Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 2015;45(1):273-286. doi:10.12775/TMNA.2015.014 apa: Graff, G., & Pilarczyk, P. (2015). An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies. https://doi.org/10.12775/TMNA.2015.014 chicago: Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis. Juliusz Schauder Center for Nonlinear Studies, 2015. https://doi.org/10.12775/TMNA.2015.014. ieee: G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds,” Topological Methods in Nonlinear Analysis, vol. 45, no. 1. Juliusz Schauder Center for Nonlinear Studies, pp. 273–286, 2015. ista: Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 45(1), 273–286. mla: Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” Topological Methods in Nonlinear Analysis, vol. 45, no. 1, Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:10.12775/TMNA.2015.014. short: G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286. date_created: 2018-12-11T11:52:44Z date_published: 2015-03-01T00:00:00Z date_updated: 2021-01-12T06:51:37Z day: '01' department: - _id: HeEd doi: 10.12775/TMNA.2015.014 intvolume: ' 45' issue: '1' language: - iso: eng month: '03' oa_version: None page: 273 - 286 publication: Topological Methods in Nonlinear Analysis publication_status: published publisher: Juliusz Schauder Center for Nonlinear Studies publist_id: '5608' quality_controlled: '1' scopus_import: 1 status: public title: An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2015' ... --- _id: '1574' abstract: - lang: eng text: Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level. acknowledgement: 'of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ' article_number: '8821' author: - first_name: Qian full_name: Chen, Qian last_name: Chen - first_name: Yang full_name: Liu, Yang last_name: Liu - first_name: Steven full_name: Maere, Steven last_name: Maere - first_name: Eunkyoung full_name: Lee, Eunkyoung last_name: Lee - first_name: Gert full_name: Van Isterdael, Gert last_name: Van Isterdael - first_name: Zidian full_name: Xie, Zidian last_name: Xie - first_name: Wei full_name: Xuan, Wei last_name: Xuan - first_name: Jessica full_name: Lucas, Jessica last_name: Lucas - first_name: Valya full_name: Vassileva, Valya last_name: Vassileva - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Niko full_name: Geldner, Niko last_name: Geldner - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jie full_name: Le, Jie last_name: Le - first_name: Hidehiro full_name: Fukaki, Hidehiro last_name: Fukaki - first_name: Erich full_name: Grotewold, Erich last_name: Grotewold - first_name: Chuanyou full_name: Li, Chuanyou last_name: Li - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Fred full_name: Sack, Fred last_name: Sack - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821 apa: Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821 chicago: Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821. ieee: Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821. mla: Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821. short: Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:48Z date_published: 2015-11-18T00:00:00Z date_updated: 2021-01-12T06:51:42Z day: '18' ddc: - '580' department: - _id: EvBe - _id: JiFr doi: 10.1038/ncomms9821 file: - access_level: open_access checksum: 8ff5c108899b548806e1cb7a302fe76d content_type: application/pdf creator: system date_created: 2018-12-12T10:14:32Z date_updated: 2020-07-14T12:45:02Z file_id: '5085' file_name: IST-2016-477-v1+1_ncomms9821.pdf file_size: 1701815 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5597' pubrep_id: '477' quality_controlled: '1' scopus_import: 1 status: public title: A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development 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: 6 year: '2015' ... --- _id: '1575' abstract: - lang: eng text: The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space. acknowledgement: M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie). article_number: '7526' author: - first_name: Mélanie full_name: Chabaud, Mélanie last_name: Chabaud - first_name: Mélina full_name: Heuzé, Mélina last_name: Heuzé - first_name: Marine full_name: Bretou, Marine last_name: Bretou - first_name: Pablo full_name: Vargas, Pablo last_name: Vargas - first_name: Paolo full_name: Maiuri, Paolo last_name: Maiuri - first_name: Paola full_name: Solanes, Paola last_name: Solanes - first_name: Mathieu full_name: Maurin, Mathieu last_name: Maurin - first_name: Emmanuel full_name: Terriac, Emmanuel last_name: Terriac - first_name: Maël full_name: Le Berre, Maël last_name: Le Berre - first_name: Danielle full_name: Lankar, Danielle last_name: Lankar - first_name: Tristan full_name: Piolot, Tristan last_name: Piolot - first_name: Robert full_name: Adelstein, Robert last_name: Adelstein - first_name: Yingfan full_name: Zhang, Yingfan last_name: Zhang - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Jordan full_name: Jacobelli, Jordan last_name: Jacobelli - first_name: Olivier full_name: Bénichou, Olivier last_name: Bénichou - first_name: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez - first_name: Matthieu full_name: Piel, Matthieu last_name: Piel - first_name: Ana full_name: Lennon Duménil, Ana last_name: Lennon Duménil citation: ama: Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526 apa: Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526 chicago: Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526. ieee: M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526. mla: Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526. short: M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:48Z date_published: 2015-06-25T00:00:00Z date_updated: 2021-01-12T06:51:42Z day: '25' ddc: - '570' department: - _id: MiSi doi: 10.1038/ncomms8526 file: - access_level: open_access checksum: bae12e86be2adb28253f890b8bba8315 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:58Z date_updated: 2020-07-14T12:45:02Z file_id: '4915' file_name: IST-2016-476-v1+1_ncomms8526.pdf file_size: 4530215 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5596' pubrep_id: '476' quality_controlled: '1' scopus_import: 1 status: public title: Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ...