--- _id: '7400' abstract: - lang: eng text: 'Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.' article_processing_charge: No article_type: original author: - first_name: Paris full_name: Veltsos, Paris last_name: Veltsos - first_name: Kate E. full_name: Ridout, Kate E. last_name: Ridout - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Santiago C. full_name: González-Martínez, Santiago C. last_name: González-Martínez - first_name: Aline full_name: Muyle, Aline last_name: Muyle - first_name: Olivier full_name: Emery, Olivier last_name: Emery - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Vojtech full_name: Hudzieczek, Vojtech last_name: Hudzieczek - first_name: Roman full_name: Hobza, Roman last_name: Hobza - first_name: Boris full_name: Vyskot, Boris last_name: Vyskot - first_name: Gabriel A. B. full_name: Marais, Gabriel A. B. last_name: Marais - first_name: Dmitry A. full_name: Filatov, Dmitry A. last_name: Filatov - first_name: John R. full_name: Pannell, John R. last_name: Pannell citation: ama: Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 2019;212(3):815-835. doi:10.1534/genetics.119.302045 apa: Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.119.302045 chicago: Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/genetics.119.302045. ieee: P. Veltsos et al., “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” Genetics, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019. ista: Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835. mla: Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:10.1534/genetics.119.302045. short: P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835. date_created: 2020-01-29T16:15:44Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-09-07T14:49:29Z day: '01' department: - _id: BeVi doi: 10.1534/genetics.119.302045 ec_funded: 1 external_id: isi: - '000474809300015' pmid: - '31113811' intvolume: ' 212' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1534/genetics.119.302045 month: '07' oa: 1 oa_version: Published Version page: 815-835 pmid: 1 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Genetics publication_identifier: eissn: - 1943-2631 issn: - 0016-6731 publication_status: published publisher: Genetics Society of America quality_controlled: '1' scopus_import: '1' status: public title: Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 212 year: '2019' ... --- _id: '7404' abstract: - lang: eng text: The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation. article_number: dev171397 article_processing_charge: No article_type: original author: - first_name: Tomke full_name: Stürner, Tomke last_name: Stürner - first_name: Anastasia full_name: Tatarnikova, Anastasia last_name: Tatarnikova - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Barbara full_name: Schaffran, Barbara last_name: Schaffran - first_name: Hermann full_name: Cuntz, Hermann last_name: Cuntz - first_name: Yun full_name: Zhang, Yun last_name: Zhang - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Sven full_name: Bogdan, Sven last_name: Bogdan - first_name: Vic full_name: Small, Vic last_name: Small - first_name: Gaia full_name: Tavosanis, Gaia last_name: Tavosanis citation: ama: Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 2019;146(7). doi:10.1242/dev.171397 apa: Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. The Company of Biologists. https://doi.org/10.1242/dev.171397 chicago: Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.171397. ieee: T. Stürner et al., “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” Development, vol. 146, no. 7. The Company of Biologists, 2019. ista: Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397. mla: Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development, vol. 146, no. 7, dev171397, The Company of Biologists, 2019, doi:10.1242/dev.171397. short: T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019). date_created: 2020-01-29T16:27:10Z date_published: 2019-04-04T00:00:00Z date_updated: 2023-09-07T14:47:00Z day: '04' department: - _id: MiSi doi: 10.1242/dev.171397 external_id: isi: - '000464583200006' pmid: - '30910826' intvolume: ' 146' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1242/dev.171397 month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Development publication_identifier: eissn: - 1477-9129 issn: - 0950-1991 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 146 year: '2019' ... --- _id: '7402' abstract: - lang: eng text: Graph planning gives rise to fundamental algorithmic questions such as shortest path, traveling salesman problem, etc. A classical problem in discrete planning is to consider a weighted graph and construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary, to represent the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time. Consequently, our polynomial-time algorithm for adversarial stopping time also computes an optimal plan among all possible plans. 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: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: 34th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2019:1-13. doi:10.1109/lics.2019.8785706' apa: 'Chatterjee, K., & Doyen, L. (2019). Graph planning with expected finite horizon. In 34th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/lics.2019.8785706' chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” In 34th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. IEEE, 2019. https://doi.org/10.1109/lics.2019.8785706. ieee: K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” in 34th Annual ACM/IEEE Symposium on Logic in Computer Science, Vancouver, BC, Canada, 2019, pp. 1–13. ista: 'Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon. 34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.' mla: Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13, doi:10.1109/lics.2019.8785706. short: K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13. conference: end_date: 2019-06-27 location: Vancouver, BC, Canada name: 'LICS: Symposium on Logic in Computer Science' start_date: 2019-06-24 date_created: 2020-01-29T16:18:33Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T14:48:11Z day: '01' department: - _id: KrCh doi: 10.1109/lics.2019.8785706 external_id: arxiv: - '1802.03642' isi: - '000805002800001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.03642 month: '06' oa: 1 oa_version: Preprint page: 1-13 publication: 34th Annual ACM/IEEE Symposium on Logic in Computer Science publication_identifier: isbn: - '9781728136080' publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '11402' relation: later_version status: public scopus_import: '1' status: public title: Graph planning with expected finite horizon type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '7451' abstract: - lang: eng text: We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition. article_number: '150' article_processing_charge: No article_type: original author: - first_name: A. full_name: Vukics, A. last_name: Vukics - first_name: A. full_name: Dombi, A. last_name: Dombi - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: P. full_name: Domokos, P. last_name: Domokos citation: ama: Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 2019;3. doi:10.22331/q-2019-06-03-150 apa: Vukics, A., Dombi, A., Fink, J. M., & Domokos, P. (2019). Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/q-2019-06-03-150 chicago: Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. https://doi.org/10.22331/q-2019-06-03-150. ieee: A. Vukics, A. Dombi, J. M. Fink, and P. Domokos, “Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition,” Quantum, vol. 3. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. ista: Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 3, 150. mla: Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum, vol. 3, 150, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019, doi:10.22331/q-2019-06-03-150. short: A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019). date_created: 2020-02-05T09:57:57Z date_published: 2019-06-03T00:00:00Z date_updated: 2023-09-07T14:57:39Z day: '03' ddc: - '530' department: - _id: JoFi doi: 10.22331/q-2019-06-03-150 external_id: arxiv: - '1809.09737' isi: - '000469987500004' file: - access_level: open_access checksum: 26b9ba8f0155d183f1ee55295934a17f content_type: application/pdf creator: dernst date_created: 2020-02-11T09:25:23Z date_updated: 2020-07-14T12:47:58Z file_id: '7483' file_name: 2019_Quantum_Vukics.pdf file_size: 5805248 relation: main_file file_date_updated: 2020-07-14T12:47:58Z has_accepted_license: '1' intvolume: ' 3' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Quantum publication_identifier: issn: - 2521-327X publication_status: published publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften quality_controlled: '1' status: public title: Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 3 year: '2019' ... --- _id: '7468' abstract: - lang: eng text: We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems. article_number: 11138-11147 article_processing_charge: No author: - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Vol 2019-June. IEEE; 2019. doi:10.1109/CVPR.2019.01140' apa: 'Swoboda, P., & Kolmogorov, V. (2019). Map inference via block-coordinate Frank-Wolfe algorithm. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Vol. 2019–June). Long Beach, CA, United States: IEEE. https://doi.org/10.1109/CVPR.2019.01140' chicago: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Vol. 2019–June. IEEE, 2019. https://doi.org/10.1109/CVPR.2019.01140. ieee: P. Swoboda and V. Kolmogorov, “Map inference via block-coordinate Frank-Wolfe algorithm,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Long Beach, CA, United States, 2019, vol. 2019–June. ista: 'Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2019–June, 11138–11147.' mla: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, vol. 2019–June, 11138–11147, IEEE, 2019, doi:10.1109/CVPR.2019.01140. short: P. Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2019. conference: end_date: 2019-06-20 location: Long Beach, CA, United States name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2019-06-15 date_created: 2020-02-09T23:00:52Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-07T14:54:24Z day: '01' department: - _id: VlKo doi: 10.1109/CVPR.2019.01140 ec_funded: 1 external_id: arxiv: - '1806.05049' isi: - '000542649304076' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.05049 month: '06' oa: 1 oa_version: Preprint project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition publication_identifier: isbn: - '9781728132938' issn: - '10636919' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Map inference via block-coordinate Frank-Wolfe algorithm type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2019-June year: '2019' ...