--- _id: '988' abstract: - lang: eng text: The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement. article_processing_charge: No author: - first_name: Gaurav full_name: Nanda, Gaurav last_name: Nanda - first_name: Juan L full_name: Aguilera Servin, Juan L id: 2A67C376-F248-11E8-B48F-1D18A9856A87 last_name: Aguilera Servin orcid: 0000-0002-2862-8372 - first_name: Péter full_name: Rakyta, Péter last_name: Rakyta - first_name: Andor full_name: Kormányos, Andor last_name: Kormányos - first_name: Reinhold full_name: Kleiner, Reinhold last_name: Kleiner - first_name: Dieter full_name: Koelle, Dieter last_name: Koelle - first_name: Kazuo full_name: Watanabe, Kazuo last_name: Watanabe - first_name: Takashi full_name: Taniguchi, Takashi last_name: Taniguchi - first_name: Lieven full_name: Vandersypen, Lieven last_name: Vandersypen - first_name: Srijit full_name: Goswami, Srijit last_name: Goswami citation: ama: Nanda G, Aguilera Servin JL, Rakyta P, et al. Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. 2017;17(6):3396-3401. doi:10.1021/acs.nanolett.7b00097 apa: Nanda, G., Aguilera Servin, J. L., Rakyta, P., Kormányos, A., Kleiner, R., Koelle, D., … Goswami, S. (2017). Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b00097 chicago: Nanda, Gaurav, Juan L Aguilera Servin, Péter Rakyta, Andor Kormányos, Reinhold Kleiner, Dieter Koelle, Kazuo Watanabe, Takashi Taniguchi, Lieven Vandersypen, and Srijit Goswami. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b00097. ieee: G. Nanda et al., “Current-phase relation of ballistic graphene Josephson junctions,” Nano Letters, vol. 17, no. 6. American Chemical Society, pp. 3396–3401, 2017. ista: Nanda G, Aguilera Servin JL, Rakyta P, Kormányos A, Kleiner R, Koelle D, Watanabe K, Taniguchi T, Vandersypen L, Goswami S. 2017. Current-phase relation of ballistic graphene Josephson junctions. Nano Letters. 17(6), 3396–3401. mla: Nanda, Gaurav, et al. “Current-Phase Relation of Ballistic Graphene Josephson Junctions.” Nano Letters, vol. 17, no. 6, American Chemical Society, 2017, pp. 3396–401, doi:10.1021/acs.nanolett.7b00097. short: G. Nanda, J.L. Aguilera Servin, P. Rakyta, A. Kormányos, R. Kleiner, D. Koelle, K. Watanabe, T. Taniguchi, L. Vandersypen, S. Goswami, Nano Letters 17 (2017) 3396–3401. date_created: 2018-12-11T11:49:33Z date_published: 2017-05-05T00:00:00Z date_updated: 2023-09-22T09:56:21Z day: '05' ddc: - '621' department: - _id: NanoFab doi: 10.1021/acs.nanolett.7b00097 external_id: isi: - '000403631600011' file: - access_level: open_access checksum: 22021daa90cf13b01becd776838acb7b content_type: application/pdf creator: system date_created: 2018-12-12T10:13:50Z date_updated: 2020-07-14T12:48:18Z file_id: '5037' file_name: IST-2017-826-v1+1_2017_Aguilera-Servin_Current.pdf file_size: 508638 relation: main_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '6' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 3396 - 3401 publication: Nano Letters publication_identifier: issn: - '15306984' publication_status: published publisher: American Chemical Society publist_id: '6412' pubrep_id: '826' quality_controlled: '1' scopus_import: '1' status: public title: Current-phase relation of ballistic graphene Josephson junctions 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 17 year: '2017' ... --- _id: '993' abstract: - lang: eng text: In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development. article_number: '15140' article_processing_charge: Yes (in subscription journal) author: - first_name: Anna full_name: Levina (Martius), Anna id: 35AF8020-F248-11E8-B48F-1D18A9856A87 last_name: Levina (Martius) - first_name: Viola full_name: Priesemann, Viola last_name: Priesemann citation: ama: Levina (Martius) A, Priesemann V. Subsampling scaling. Nature Communications. 2017;8. doi:10.1038/ncomms15140 apa: Levina (Martius), A., & Priesemann, V. (2017). Subsampling scaling. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15140 chicago: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15140. ieee: A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140. mla: Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” Nature Communications, vol. 8, 15140, Nature Publishing Group, 2017, doi:10.1038/ncomms15140. short: A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017). date_created: 2018-12-11T11:49:35Z date_published: 2017-05-04T00:00:00Z date_updated: 2023-09-22T09:54:07Z day: '04' ddc: - '005' - '571' department: - _id: GaTk - _id: JoCs doi: 10.1038/ncomms15140 ec_funded: 1 external_id: isi: - '000400560700001' file: - access_level: open_access checksum: 9880212f8c4c53404c7c6fbf9023c53a content_type: application/pdf creator: system date_created: 2018-12-12T10:15:05Z date_updated: 2020-07-14T12:48:19Z file_id: '5122' file_name: IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf file_size: 746224 relation: main_file file_date_updated: 2020-07-14T12:48:19Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '05' 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: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6406' pubrep_id: '819' quality_controlled: '1' scopus_import: '1' status: public title: Subsampling scaling 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: 8 year: '2017' ... --- _id: '995' abstract: - lang: eng text: Recently it was shown that an impurity exchanging orbital angular momentum with a surrounding bath can be described in terms of the angulon quasiparticle [Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor dressed by a many-particle field of boson excitations, and can be formed out of, for example, a molecule or a nonspherical atom in superfluid helium, or out of an electron coupled to lattice phonons or a Bose condensate. Here we develop an approach to the angulon based on the path-integral formalism, which sets the ground for a systematic, perturbative treatment of the angulon problem. The resulting perturbation series can be interpreted in terms of Feynman diagrams, from which, in turn, one can derive a set of diagrammatic rules. These rules extend the machinery of the graphical theory of angular momentum - well known from theoretical atomic spectroscopy - to the case where an environment with an infinite number of degrees of freedom is present. In particular, we show that each diagram can be interpreted as a 'skeleton', which enforces angular momentum conservation, dressed by an additional many-body contribution. This connection between the angulon theory and the graphical theory of angular momentum is particularly important as it allows to systematically and substantially simplify the analytical representation of each diagram. In order to exemplify the technique, we calculate the 1- and 2-loop contributions to the angulon self-energy, the spectral function, and the quasiparticle weight. The diagrammatic theory we develop paves the way to investigate next-to-leading order quantities in a more compact way compared to the variational approaches. article_number: '085410' article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Bighin G, Lemeshko M. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. 2017;96(8). doi:10.1103/PhysRevB.96.085410 apa: Bighin, G., & Lemeshko, M. (2017). Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.085410 chicago: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.085410. ieee: G. Bighin and M. Lemeshko, “Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 8. American Physical Society, 2017. ista: Bighin G, Lemeshko M. 2017. Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment. Physical Review B - Condensed Matter and Materials Physics. 96(8), 085410. mla: Bighin, Giacomo, and Mikhail Lemeshko. “Diagrammatic Approach to Orbital Quantum Impurities Interacting with a Many-Particle Environment.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 8, 085410, American Physical Society, 2017, doi:10.1103/PhysRevB.96.085410. short: G. Bighin, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 96 (2017). date_created: 2018-12-11T11:49:36Z date_published: 2017-08-07T00:00:00Z date_updated: 2023-09-22T09:53:17Z day: '07' department: - _id: MiLe doi: 10.1103/PhysRevB.96.085410 external_id: isi: - '000407017100009' intvolume: ' 96' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.02616 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - '24699950' publication_status: published publisher: American Physical Society publist_id: '6404' quality_controlled: '1' scopus_import: '1' status: public title: Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 96 year: '2017' ... --- _id: '989' abstract: - lang: eng text: We present a generalized optimal transport model in which the mass-preserving constraint for the L2-Wasserstein distance is relaxed by introducing a source term in the continuity equation. The source term is also incorporated in the path energy by means of its squared L2-norm in time of a functional with linear growth in space. This extension of the original transport model enables local density modulations, which is a desirable feature in applications such as image warping and blending. A key advantage of the use of a functional with linear growth in space is that it allows for singular sources and sinks, which can be supported on points or lines. On a technical level, the L2-norm in time ensures a disintegration of the source in time, which we use to obtain the well-posedness of the model and the existence of geodesic paths. The numerical discretization is based on the proximal splitting approach [18] and selected numerical test cases show the potential of the proposed approach. Furthermore, the approach is applied to the warping and blending of textures. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Martin full_name: Rumpf, Martin last_name: Rumpf - first_name: Stefan full_name: Simon, Stefan last_name: Simon citation: ama: 'Maas J, Rumpf M, Simon S. Transport based image morphing with intensity modulation. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:563-577. doi:10.1007/978-3-319-58771-4_45' apa: 'Maas, J., Rumpf, M., & Simon, S. (2017). Transport based image morphing with intensity modulation. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 563–577). Presented at the SSVM:  Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_45' chicago: Maas, Jan, Martin Rumpf, and Stefan Simon. “Transport Based Image Morphing with Intensity Modulation.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:563–77. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_45. ieee: J. Maas, M. Rumpf, and S. Simon, “Transport based image morphing with intensity modulation,” presented at the SSVM:  Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 563–577. ista: Maas J, Rumpf M, Simon S. 2017. Transport based image morphing with intensity modulation. SSVM:  Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 563–577. mla: Maas, Jan, et al. Transport Based Image Morphing with Intensity Modulation. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 563–77, doi:10.1007/978-3-319-58771-4_45. short: J. Maas, M. Rumpf, S. Simon, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 563–577. conference: end_date: 2017-06-08 location: Kolding, Denmark name: 'SSVM: Scale Space and Variational Methods in Computer Vision' start_date: 2017-06-04 date_created: 2018-12-11T11:49:34Z date_published: 2017-05-18T00:00:00Z date_updated: 2023-09-22T09:55:50Z day: '18' department: - _id: JaMa doi: 10.1007/978-3-319-58771-4_45 editor: - first_name: François full_name: Lauze, François last_name: Lauze - first_name: Yiqiu full_name: Dong, Yiqiu last_name: Dong - first_name: Anders full_name: Bjorholm Dahl, Anders last_name: Bjorholm Dahl external_id: isi: - '000432210900045' intvolume: ' 10302' isi: 1 language: - iso: eng month: '05' oa_version: None page: 563 - 577 publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6410' quality_controlled: '1' scopus_import: '1' status: public title: Transport based image morphing with intensity modulation type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10302 year: '2017' ... --- _id: '994' abstract: - lang: eng text: The formation of vortices is usually considered to be the main mechanism of angular momentum disposal in superfluids. Recently, it was predicted that a superfluid can acquire angular momentum via an alternative, microscopic route -- namely, through interaction with rotating impurities, forming so-called `angulon quasiparticles' [Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to transfer of a small number of angular momentum quanta from the impurity to the superfluid, as opposed to vortex instabilities, where angular momentum is quantized in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules) represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically 3D as well, as opposed to a merely planar rotation which is inherent to vortices. Herein we show that the angulon theory can explain the anomalous broadening of the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities in experiment. article_processing_charge: No author: - first_name: Igor full_name: Cherepanov, Igor id: 339C7E5A-F248-11E8-B48F-1D18A9856A87 last_name: Cherepanov - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Cherepanov I, Lemeshko M. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 2017;1(3). doi:10.1103/PhysRevMaterials.1.035602 apa: Cherepanov, I., & Lemeshko, M. (2017). Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.1.035602 chicago: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials. American Physical Society, 2017. https://doi.org/10.1103/PhysRevMaterials.1.035602. ieee: I. Cherepanov and M. Lemeshko, “Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules,” Physical Review Materials, vol. 1, no. 3. American Physical Society, 2017. ista: Cherepanov I, Lemeshko M. 2017. Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules. Physical Review Materials. 1(3). mla: Cherepanov, Igor, and Mikhail Lemeshko. “Fingerprints of Angulon Instabilities in the Spectra of Matrix-Isolated Molecules.” Physical Review Materials, vol. 1, no. 3, American Physical Society, 2017, doi:10.1103/PhysRevMaterials.1.035602. short: I. Cherepanov, M. Lemeshko, Physical Review Materials 1 (2017). date_created: 2018-12-11T11:49:35Z date_published: 2017-08-08T00:00:00Z date_updated: 2023-09-22T09:53:42Z day: '08' department: - _id: MiLe doi: 10.1103/PhysRevMaterials.1.035602 ec_funded: 1 external_id: isi: - '000416564000004' intvolume: ' 1' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.09220 month: '08' oa: 1 oa_version: Submitted Version project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Physical Review Materials publication_status: published publisher: American Physical Society publist_id: '6405' quality_controlled: '1' scopus_import: '1' status: public title: Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 1 year: '2017' ... --- _id: '991' abstract: - lang: eng text: Synaptotagmin 7 (Syt7) was originally identified as a slow Ca2+ sensor for lysosome fusion, but its function at fast synapses is controversial. The paper by Luo and Südhof (2017) in this issue of Neuron shows that at the calyx of Held in the auditory brainstem Syt7 triggers asynchronous release during stimulus trains, resulting in reliable and temporally precise high-frequency transmission. Thus, a slow Ca2+ sensor contributes to the fast signaling properties of the calyx synapse. article_processing_charge: No author: - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Chen C, Jonas PM. Synaptotagmins: That’s why so many. Neuron. 2017;94(4):694-696. doi:10.1016/j.neuron.2017.05.011' apa: 'Chen, C., & Jonas, P. M. (2017). Synaptotagmins: That’s why so many. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.05.011' chicago: 'Chen, Chong, and Peter M Jonas. “Synaptotagmins: That’s Why so Many.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.05.011.' ieee: 'C. Chen and P. M. Jonas, “Synaptotagmins: That’s why so many,” Neuron, vol. 94, no. 4. Elsevier, pp. 694–696, 2017.' ista: 'Chen C, Jonas PM. 2017. Synaptotagmins: That’s why so many. Neuron. 94(4), 694–696.' mla: 'Chen, Chong, and Peter M. Jonas. “Synaptotagmins: That’s Why so Many.” Neuron, vol. 94, no. 4, Elsevier, 2017, pp. 694–96, doi:10.1016/j.neuron.2017.05.011.' short: C. Chen, P.M. Jonas, Neuron 94 (2017) 694–696. date_created: 2018-12-11T11:49:34Z date_published: 2017-05-17T00:00:00Z date_updated: 2023-09-22T09:54:37Z day: '17' department: - _id: PeJo doi: 10.1016/j.neuron.2017.05.011 external_id: isi: - '000401415100002' intvolume: ' 94' isi: 1 issue: '4' language: - iso: eng month: '05' oa_version: None page: 694 - 696 publication: Neuron publication_identifier: issn: - '08966273' publication_status: published publisher: Elsevier publist_id: '6408' quality_controlled: '1' scopus_import: '1' status: public title: 'Synaptotagmins: That’s why so many' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 94 year: '2017' ... --- _id: '954' abstract: - lang: eng text: Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for. article_number: e25192 article_processing_charge: Yes author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - 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: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192 apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192 chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192. ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192. mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192. short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-05-18T00:00:00Z date_updated: 2023-09-22T10:01:17Z day: '18' ddc: - '576' department: - _id: CaGu - _id: NiBa - _id: JoBo doi: 10.7554/eLife.25192 ec_funded: 1 external_id: isi: - '000404024800001' file: - access_level: open_access checksum: 59cdd4400fb41280122d414fea971546 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:49Z date_updated: 2020-07-14T12:48:16Z file_id: '5306' file_name: IST-2017-841-v1+1_elife-25192-v2.pdf file_size: 2441529 relation: main_file - access_level: open_access checksum: b69024880558b858eb8c5d47a92b6377 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:50Z date_updated: 2020-07-14T12:48:16Z file_id: '5307' file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf file_size: 3752660 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '6460' pubrep_id: '841' quality_controlled: '1' scopus_import: '1' status: public title: On the mechanistic nature of epistasis in a canonical cis-regulatory element 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: 6 year: '2017' ... --- _id: '955' abstract: - lang: eng text: 'Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.' article_number: '216' article_processing_charge: Yes (in subscription journal) author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - 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: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8 apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8 chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8. ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216. mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8. short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-08-09T00:00:00Z date_updated: 2023-09-22T10:00:49Z day: '09' ddc: - '539' - '576' department: - _id: GaTk - _id: NiBa doi: 10.1038/s41467-017-00238-8 ec_funded: 1 external_id: isi: - '000407198800005' file: - access_level: open_access checksum: 29a1b5db458048d3bd5c67e0e2a56818 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:14Z date_updated: 2020-07-14T12:48:16Z file_id: '5064' file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf file_size: 998157 relation: main_file - access_level: open_access checksum: 7b78401e52a576cf3e6bbf8d0abadc17 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:15Z date_updated: 2020-07-14T12:48:16Z file_id: '5065' file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf file_size: 9715993 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '08' 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 - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6459' pubrep_id: '864' quality_controlled: '1' related_material: record: - id: '6071' relation: dissertation_contains status: public scopus_import: '1' status: public title: Evolution of new regulatory functions on biophysically realistic fitness landscapes 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: 8 year: '2017' ... --- _id: '962' abstract: - lang: eng text: 'We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Minh full_name: Trinh, Minh last_name: Trinh - first_name: Duc Hiep full_name: Chu, Duc Hiep id: 3598E630-F248-11E8-B48F-1D18A9856A87 last_name: Chu - first_name: Joxan full_name: Jaffar, Joxan last_name: Jaffar citation: ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21' apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21' chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_21. ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 399–418.' ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings. CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.' mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418, doi:10.1007/978-3-319-63390-9_21. short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 399–418. conference: end_date: 2017-07-28 location: Heidelberg, Germany name: 'CAV: Computer Aided Verification' start_date: 2017-07-24 date_created: 2018-12-11T11:49:26Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-22T09:58:02Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-63390-9_21 editor: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Viktor full_name: Kunčak, Viktor last_name: Kunčak external_id: isi: - '000431900900021' intvolume: ' 10427' isi: 1 language: - iso: eng month: '01' oa_version: None page: 399 - 418 project: - _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: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6443' quality_controlled: '1' scopus_import: '1' status: public title: Model counting for recursively-defined strings type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10427 year: '2017' ... --- _id: '953' abstract: - lang: eng text: 'The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today''s understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.' article_number: '20162864' article_processing_charge: No author: - first_name: Deborah full_name: Charlesworth, Deborah last_name: Charlesworth - 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: Brian full_name: Charlesworth, Brian last_name: Charlesworth citation: ama: Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 2017;284(1855). doi:10.1098/rspb.2016.2864 apa: Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864 chicago: Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864. ieee: D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855. Royal Society, The, 2017. ista: Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864. mla: Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864. short: D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017). date_created: 2018-12-11T11:49:23Z date_published: 2017-05-31T00:00:00Z date_updated: 2023-09-22T10:01:48Z day: '31' department: - _id: NiBa doi: 10.1098/rspb.2016.2864 external_id: isi: - '000405148800021' pmid: - '28566483' intvolume: ' 284' isi: 1 issue: '1855' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/ month: '05' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '6462' quality_controlled: '1' scopus_import: '1' status: public title: The sources of adaptive evolution type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 284 year: '2017' ... --- _id: '959' abstract: - lang: eng text: In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions. article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419 apa: De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419 chicago: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419. ieee: D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p. 062419, 2017. ista: De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419. mla: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419. short: D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 062419. date_created: 2018-12-11T11:49:25Z date_published: 2017-06-28T00:00:00Z date_updated: 2023-09-22T09:59:01Z day: '28' department: - _id: GaTk doi: 10.1103/PhysRevE.95.062419 ec_funded: 1 external_id: isi: - '000404546400004' intvolume: ' 95' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/pdf/1703.00853.pdf month: '06' oa: 1 oa_version: Submitted Version page: '062419' project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics ' publication_identifier: issn: - '24700045' publication_status: published publisher: American Institute of Physics publist_id: '6446' quality_controlled: '1' scopus_import: '1' status: public title: Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 95 year: '2017' ... --- _id: '956' abstract: - lang: eng text: We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance. article_processing_charge: No author: - first_name: Eric full_name: Carlen, Eric last_name: Carlen - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869. doi:10.1016/j.jfa.2017.05.003 apa: Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003 chicago: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis. Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003. ieee: E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” Journal of Functional Analysis, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017. ista: Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869. mla: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003. short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869. date_created: 2018-12-11T11:49:24Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-22T10:00:18Z day: '01' department: - _id: JaMa doi: 10.1016/j.jfa.2017.05.003 external_id: isi: - '000406082300005' intvolume: ' 273' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.01254 month: '09' oa: 1 oa_version: Submitted Version page: 1810 - 1869 publication: Journal of Functional Analysis publication_identifier: issn: - '00221236' publication_status: published publisher: Academic Press publist_id: '6452' quality_controlled: '1' scopus_import: '1' status: public title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 273 year: '2017' ... --- _id: '952' abstract: - lang: eng text: A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area. article_processing_charge: No author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003' apa: 'Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003' chicago: 'Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.' ieee: 'M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.' ista: 'Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.' mla: 'Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.' short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60. date_created: 2018-12-11T11:49:22Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-22T10:02:21Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2017.03.003 external_id: pmid: - '28411063' file: - access_level: open_access checksum: 9aeff86fa7de69f7a15cf4fc60d57d01 content_type: application/pdf creator: dernst date_created: 2019-04-17T06:39:45Z date_updated: 2020-07-14T12:48:16Z file_id: '6327' file_name: 2017_TheoreticalPopulationBio_Turelli.pdf file_size: 2073856 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 115' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 45 - 60 pmid: 1 publication: Theoretical Population Biology publication_identifier: issn: - '00405809' publication_status: published publisher: Elsevier publist_id: '6463' pubrep_id: '972' quality_controlled: '1' scopus_import: '1' status: public title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2017' ... --- _id: '951' abstract: - lang: eng text: Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo article_number: e2001894 article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - 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: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894. ieee: T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894. mla: Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017). date_created: 2018-12-11T11:49:22Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:52Z day: '30' ddc: - '576' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894 external_id: isi: - '000402520000012' file: - access_level: open_access checksum: 107d290bd1159ec77b734eb2824b01c8 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:30Z date_updated: 2020-07-14T12:48:16Z file_id: '4691' file_name: IST-2017-843-v1+1_journal.pbio.2001894.pdf file_size: 5541206 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: PLoS Biology publication_identifier: issn: - '15449173' publication_status: published publisher: Public Library of Science publist_id: '6464' pubrep_id: '843' quality_controlled: '1' related_material: record: - id: '9856' relation: research_data status: public - id: '9857' relation: research_data status: public - id: '9858' relation: research_data status: public scopus_import: '1' status: public title: Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti 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: 15 year: '2017' ... --- _id: '947' abstract: - lang: eng text: Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence. article_number: '010401' article_processing_charge: No author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Fabrizio full_name: Capuani, Fabrizio last_name: Capuani - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino citation: ama: De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.010401 apa: De Martino, D., Capuani, F., & De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.010401 chicago: De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.010401. ieee: D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017. ista: De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 010401. mla: De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 010401, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.010401. short: D. De Martino, F. Capuani, A. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017). date_created: 2018-12-11T11:49:21Z date_published: 2017-07-10T00:00:00Z date_updated: 2023-09-22T10:03:50Z day: '10' department: - _id: GaTk doi: 10.1103/PhysRevE.96.010401 ec_funded: 1 external_id: isi: - '000405194200002' intvolume: ' 96' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.00219 month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics ' publication_identifier: issn: - '24700045' publication_status: published publisher: American Institute of Physics publist_id: '6470' quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the entropic cost of cellular growth control type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 96 year: '2017' ... --- _id: '9858' article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - 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: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016. ieee: T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016. mla: Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017). date_created: 2021-08-10T07:47:07Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:51Z day: '30' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894.s016 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '951' relation: used_in_publication status: public status: public title: Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9857' article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - 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: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015. ieee: T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015. mla: Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017). date_created: 2021-08-10T07:41:52Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:51Z day: '30' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894.s015 month: '05' oa_version: Published Version publisher: 'Public Library of Science ' related_material: record: - id: '951' relation: used_in_publication status: public status: public title: Supporting information concerning observed wMel frequencies and analyses of habitat variables type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9856' article_processing_charge: No author: - first_name: Tom full_name: Schmidt, Tom last_name: Schmidt - 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: Gordana full_name: Rasic, Gordana last_name: Rasic - first_name: Andrew full_name: Turley, Andrew last_name: Turley - first_name: Brian full_name: Montgomery, Brian last_name: Montgomery - first_name: Inaki full_name: Iturbe Ormaetxe, Inaki last_name: Iturbe Ormaetxe - first_name: Peter full_name: Cook, Peter last_name: Cook - first_name: Peter full_name: Ryan, Peter last_name: Ryan - first_name: Scott full_name: Ritchie, Scott last_name: Ritchie - first_name: Ary full_name: Hoffmann, Ary last_name: Hoffmann - first_name: Scott full_name: O’Neill, Scott last_name: O’Neill - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014 apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting Information concerning additional likelihood analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014 chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014. ieee: T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017. ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting Information concerning additional likelihood analyses and results, Public Library of Science, 10.1371/journal.pbio.2001894.s014. mla: Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014. short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017). date_created: 2021-08-10T07:36:04Z date_published: 2017-05-30T00:00:00Z date_updated: 2023-09-22T10:02:51Z day: '30' department: - _id: NiBa doi: 10.1371/journal.pbio.2001894.s014 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '951' relation: used_in_publication status: public status: public title: Supporting Information concerning additional likelihood analyses and results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '945' abstract: - lang: eng text: While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera. article_processing_charge: Yes (in subscription journal) author: - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190 apa: Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190 chicago: Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2017. https://doi.org/10.1093/molbev/msx190. ieee: A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017. ista: Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649. mla: Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190. short: A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649. date_created: 2018-12-11T11:49:20Z date_published: 2017-07-06T00:00:00Z date_updated: 2023-09-26T15:36:34Z day: '06' ddc: - '570' - '576' department: - _id: BeVi doi: 10.1093/molbev/msx190 external_id: isi: - '000411814800016' file: - access_level: open_access checksum: 009fd68043211d645ceb9d1de28274f2 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:23Z date_updated: 2020-07-14T12:48:15Z file_id: '4810' file_name: IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf file_size: 462863 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '10' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2637 - 2649 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Molecular Biology and Evolution publication_identifier: issn: - '07374038' publication_status: published publisher: Oxford University Press publist_id: '6472' pubrep_id: '848' quality_controlled: '1' scopus_import: '1' status: public title: Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 34 year: '2017' ... --- _id: '751' abstract: - lang: eng text: The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components. article_processing_charge: No author: - first_name: Yutaka full_name: Matsubayashi, Yutaka last_name: Matsubayashi - first_name: Adam full_name: Louani, Adam last_name: Louani - first_name: Anca full_name: Dragu, Anca last_name: Dragu - first_name: Besaiz full_name: Sanchez Sanchez, Besaiz last_name: Sanchez Sanchez - first_name: Eduardo full_name: Serna Morales, Eduardo last_name: Serna Morales - first_name: Lawrence full_name: Yolland, Lawrence last_name: Yolland - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Gema full_name: Vizcay, Gema last_name: Vizcay - first_name: Roland full_name: Fleck, Roland last_name: Fleck - first_name: John full_name: Heddleston, John last_name: Heddleston - first_name: Teng full_name: Chew, Teng last_name: Chew - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Brian full_name: Stramer, Brian last_name: Stramer citation: ama: Matsubayashi Y, Louani A, Dragu A, et al. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 2017;27(22):3526-3534e.4. doi:10.1016/j.cub.2017.10.001 apa: Matsubayashi, Y., Louani, A., Dragu, A., Sanchez Sanchez, B., Serna Morales, E., Yolland, L., … Stramer, B. (2017). A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.10.001 chicago: Matsubayashi, Yutaka, Adam Louani, Anca Dragu, Besaiz Sanchez Sanchez, Eduardo Serna Morales, Lawrence Yolland, Attila György, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.10.001. ieee: Y. Matsubayashi et al., “A moving source of matrix components is essential for De Novo basement membrane formation,” Current Biology, vol. 27, no. 22. Cell Press, p. 3526–3534e.4, 2017. ista: Matsubayashi Y, Louani A, Dragu A, Sanchez Sanchez B, Serna Morales E, Yolland L, György A, Vizcay G, Fleck R, Heddleston J, Chew T, Siekhaus DE, Stramer B. 2017. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 27(22), 3526–3534e.4. mla: Matsubayashi, Yutaka, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” Current Biology, vol. 27, no. 22, Cell Press, 2017, p. 3526–3534e.4, doi:10.1016/j.cub.2017.10.001. short: Y. Matsubayashi, A. Louani, A. Dragu, B. Sanchez Sanchez, E. Serna Morales, L. Yolland, A. György, G. Vizcay, R. Fleck, J. Heddleston, T. Chew, D.E. Siekhaus, B. Stramer, Current Biology 27 (2017) 3526–3534e.4. date_created: 2018-12-11T11:48:18Z date_published: 2017-11-09T00:00:00Z date_updated: 2023-09-27T12:25:31Z day: '09' ddc: - '570' - '576' department: - _id: DaSi doi: 10.1016/j.cub.2017.10.001 external_id: isi: - '000415815800031' file: - access_level: open_access checksum: 264cf6c6c3551486ba5ea786850e000a content_type: application/pdf creator: system date_created: 2018-12-12T10:09:45Z date_updated: 2020-07-14T12:47:59Z file_id: '4770' file_name: IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf file_size: 4770657 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 3526 - 3534e.4 publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press publist_id: '6905' pubrep_id: '875' quality_controlled: '1' scopus_import: '1' status: public title: A moving source of matrix components is essential for De Novo basement membrane formation 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: 27 year: '2017' ...