--- OA_type: closed access _id: '1979' abstract: - lang: eng text: NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine. article_processing_charge: No article_type: original author: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Sazanov LA. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 2014;46(4):247-253. doi:10.1007/s10863-014-9554-z apa: Sazanov, L. A. (2014). The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. Springer Nature. https://doi.org/10.1007/s10863-014-9554-z chicago: Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes. Springer Nature, 2014. https://doi.org/10.1007/s10863-014-9554-z. ieee: L. A. Sazanov, “The mechanism of coupling between electron transfer and proton translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4. Springer Nature, pp. 247–253, 2014. ista: Sazanov LA. 2014. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes. 46(4), 247–253. mla: Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and Biomembranes, vol. 46, no. 4, Springer Nature, 2014, pp. 247–53, doi:10.1007/s10863-014-9554-z. short: L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253. date_created: 2018-12-11T11:55:01Z date_published: 2014-08-01T00:00:00Z date_updated: 2026-09-04T11:48:14Z day: '01' doi: 10.1007/s10863-014-9554-z extern: '1' external_id: pmid: - '24943718' fulldoi: https://doi.org/10.1007/s10863-014-9554-z intvolume: ' 46' issue: '4' language: - iso: eng month: '08' oa_version: None page: 247 - 253 pmid: 1 publication: Journal of Bioenergetics and Biomembranes publication_identifier: eissn: - 1573-6881 issn: - 0145-479X publication_status: published publisher: Springer Nature publist_id: '5104' status: public title: The mechanism of coupling between electron transfer and proton translocation in respiratory complex I type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 46 year: '2014' ... --- OA_place: repository OA_type: green _id: '1761' abstract: - lang: eng text: Metal silicides formed by means of thermal annealing processes are employed as contact materials in microelectronics. Control of the structure of silicide/silicon interfaces becomes a critical issue when the characteristic size of the device is reduced below a few tens of nanometers. Here, we report on silicide clustering occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling spectroscopy. Our results provide evidence for the segregation of a PtSi cluster with a diameter of a few nanometers from the silicide contact. The cluster acts as a metallic quantum dot giving rise to distinct signatures of quantum transport through its discrete energy states. acknowledgement: This work was supported by the Agence Nationale de la Recherche and by the EU through the ERC Starting Grant HybridNano article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Massimo full_name: Mongillo, Massimo last_name: Mongillo - first_name: Panayotis full_name: Spathis, Panayotis last_name: Spathis - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi - first_name: Pascal full_name: Gentile, Pascal last_name: Gentile - first_name: Riccardo full_name: Rurali, Riccardo last_name: Rurali - first_name: Xavier full_name: Cartoixà, Xavier last_name: Cartoixà citation: ama: Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025 apa: Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali, R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025 chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi, Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X. American Physical Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025. ieee: M. Mongillo et al., “PtSi clustering in silicon probed by transport spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society, 2014. ista: Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 3(4). mla: Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025. short: M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali, X. Cartoixà, Physical Review X 3 (2014). date_created: 2018-12-11T11:53:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2026-09-04T11:52:28Z day: '01' doi: 10.1103/PhysRevX.3.041025 extern: '1' external_id: arxiv: - abs/1407.5413 fulldoi: https://doi.org/10.1103/PhysRevX.3.041025 intvolume: ' 3' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.5413 month: '01' oa: 1 oa_version: None publication: Physical Review X publication_identifier: eissn: - 2160-3308 publication_status: published publisher: American Physical Society publist_id: '5363' status: public title: PtSi clustering in silicon probed by transport spectroscopy type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 3 year: '2014' ... --- OA_type: closed access _id: '1058' abstract: - lang: eng text: Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy. article_processing_charge: No article_type: original author: - first_name: Nickels full_name: Jensen, Nickels last_name: Jensen - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Katrin full_name: Willig, Katrin last_name: Willig - first_name: Flavie full_name: Lavoie Cardinal, Flavie last_name: Lavoie Cardinal - first_name: Tanja full_name: Brakemann, Tanja last_name: Brakemann - first_name: Stefan full_name: Hell, Stefan last_name: Hell - first_name: Stefan full_name: Jakobs, Stefan last_name: Jakobs citation: ama: Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034 apa: Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034 chicago: Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034. ieee: N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014. ista: Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762. mla: Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034. short: N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762. date_created: 2018-12-11T11:49:55Z date_published: 2014-03-17T00:00:00Z date_updated: 2026-09-04T12:18:04Z day: '17' doi: 10.1002/cphc.201301034 extern: '1' external_id: pmid: - '24497300' fulldoi: https://doi.org/10.1002/cphc.201301034 intvolume: ' 15' issue: '4' language: - iso: eng month: '03' oa_version: None page: 756 - 762 pmid: 1 publication: ChemPhysChem publication_identifier: eissn: - 1439-7641 issn: - 1439-4235 publication_status: published publisher: Wiley-Blackwell publist_id: '6332' status: public title: Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2014' ... --- OA_type: closed access _id: '1312' abstract: - lang: eng text: We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long. article_processing_charge: No article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: 'Fischer JL. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818. doi:10.1007/s00205-013-0690-0' apa: 'Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-013-0690-0' chicago: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis. Springer Nature, 2014. https://doi.org/10.1007/s00205-013-0690-0.' ieee: 'J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation: The case of weak slippage,” Archive for Rational Mechanics and Analysis, vol. 211, no. 3. Springer Nature, pp. 771–818, 2014.' ista: 'Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3), 771–818.' mla: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis, vol. 211, no. 3, Springer Nature, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.' short: J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818. date_created: 2018-12-11T11:51:18Z date_published: 2014-01-01T00:00:00Z date_updated: 2026-09-04T11:54:26Z day: '01' doi: 10.1007/s00205-013-0690-0 extern: '1' fulldoi: https://doi.org/10.1007/s00205-013-0690-0 intvolume: ' 211' issue: '3' language: - iso: eng month: '01' oa_version: None page: 771 - 818 publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature publist_id: '5959' status: public title: 'Upper bounds on waiting times for the Thin-film equation: The case of weak slippage' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 211 year: '2014' ... --- OA_type: closed access _id: '1309' abstract: - lang: eng text: We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation. article_processing_charge: No article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0 apa: Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0 chicago: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0. ieee: J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models,” Nonlinear Differential Equations and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014. ista: Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 21(1), 27–50. mla: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0. short: J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014) 27–50. date_created: 2018-12-11T11:51:17Z date_published: 2014-01-01T00:00:00Z date_updated: 2026-09-04T11:56:53Z day: '01' doi: 10.1007/s00030-013-0235-0 extern: '1' fulldoi: https://doi.org/10.1007/s00030-013-0235-0 intvolume: ' 21' issue: '1' language: - iso: eng month: '01' oa_version: None page: 27 - 50 publication: Nonlinear Differential Equations and Applications publication_identifier: eissn: - 1420-9004 issn: - 1021-9722 publication_status: published publisher: Birkhäuser publist_id: '5960' status: public title: Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 21 year: '2014' ... --- OA_place: repository OA_type: green _id: '980' abstract: - lang: eng text: Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization. acknowledgement: Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. We acknowledge support by NSERC Discovery Grant (D.A.). article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Dmitry full_name: Abanin, Dmitry last_name: Abanin citation: ama: Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 2014;90(17). doi:10.1103/PhysRevB.90.174302 apa: Serbyn, M., Papić, Z., & Abanin, D. (2014). Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.174302 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.174302. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized phase,” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17. American Physical Society, 2014. ista: Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 90(17). mla: Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17, American Physical Society, 2014, doi:10.1103/PhysRevB.90.174302. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 90 (2014). date_created: 2018-12-11T11:49:31Z date_published: 2014-11-06T00:00:00Z date_updated: 2026-09-09T10:46:56Z day: '06' doi: 10.1103/PhysRevB.90.174302 extern: '1' external_id: arxiv: - abs/1408.4105 fulldoi: https://doi.org/10.1103/PhysRevB.90.174302 intvolume: ' 90' issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.4105 month: '11' oa: 1 oa_version: None publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - 1098-0121 publication_status: published publisher: American Physical Society publist_id: '6420' status: public title: Quantum quenches in the many-body localized phase type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 90 year: '2014' ... --- OA_place: repository OA_type: green _id: '978' abstract: - lang: eng text: The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications. acknowledgement: V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105 for the partial support of W.Z. and D.W. (data acquisition). Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF DMR 1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231. W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009. W-F.T. also thanks C. Fang for useful discussions. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Ilija full_name: Zeljkovic, Ilija last_name: Zeljkovic - first_name: Yoshinori full_name: Okada, Yoshinori last_name: Okada - first_name: Chengyi full_name: Huang, Chengyi last_name: Huang - first_name: Raman full_name: Sankar, Raman last_name: Sankar - first_name: Daniel full_name: Walkup, Daniel last_name: Walkup - first_name: Wenwen full_name: Zhou, Wenwen last_name: Zhou - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Fangcheng full_name: Chou, Fangcheng last_name: Chou - first_name: Wei full_name: Tsai, Wei last_name: Tsai - first_name: Hsin full_name: Lin, Hsin last_name: Lin - first_name: Arun full_name: Bansil, Arun last_name: Bansil - first_name: Liang full_name: Fu, Liang last_name: Fu - first_name: Md full_name: Hasan, Md last_name: Hasan - first_name: Vidya full_name: Madhavan, Vidya last_name: Madhavan citation: ama: Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. 2014;10(8):572-577. doi:10.1038/nphys3012 apa: Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2014). Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3012 chicago: Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” Nature Physics. Nature Publishing Group, 2014. https://doi.org/10.1038/nphys3012. ieee: I. Zeljkovic et al., “Mapping the unconventional orbital texture in topological crystalline insulators,” Nature Physics, vol. 10, no. 8. Nature Publishing Group, pp. 572–577, 2014. ista: Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. 10(8), 572–577. mla: Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” Nature Physics, vol. 10, no. 8, Nature Publishing Group, 2014, pp. 572–77, doi:10.1038/nphys3012. short: I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn, F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics 10 (2014) 572–577. date_created: 2018-12-11T11:49:30Z date_published: 2014-08-01T00:00:00Z date_updated: 2026-09-09T10:57:16Z day: '01' doi: 10.1038/nphys3012 extern: '1' external_id: arxiv: - abs/1312.0164 fulldoi: https://doi.org/10.1038/nphys3012 intvolume: ' 10' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1312.0164 month: '08' oa: 1 oa_version: None page: 572 - 577 publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Nature Publishing Group publist_id: '6423' status: public title: Mapping the unconventional orbital texture in topological crystalline insulators type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 10 year: '2014' ... --- OA_type: free access _id: '865' abstract: - lang: eng text: Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers. article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Koval, Alexey last_name: Koval - first_name: Peter full_name: Vlasov, Peter last_name: Vlasov - first_name: Polina full_name: Shichkova, Polina last_name: Shichkova - first_name: S full_name: Khunderyakova, S last_name: Khunderyakova - first_name: Yury full_name: Markov, Yury last_name: Markov - first_name: J full_name: Panchenko, J last_name: Panchenko - first_name: A full_name: Volodina, A last_name: Volodina - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Katanaev, Vladimir last_name: Katanaev citation: ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007 apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007 chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014. https://doi.org/10.1016/j.bcp.2013.12.007. ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014. ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578. mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007. short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578. date_created: 2018-12-11T11:48:55Z date_published: 2014-02-15T00:00:00Z date_updated: 2026-09-09T11:17:42Z day: '15' doi: 10.1016/j.bcp.2013.12.007 extern: '1' external_id: pmid: - '24355563' fulldoi: https://doi.org/10.1016/j.bcp.2013.12.007 intvolume: ' 87' issue: '4' language: - iso: eng month: '02' oa_version: None page: 571 - 578 pmid: 1 publication: Biochemical Pharmacology publication_identifier: eissn: - 1873-2968 issn: - 0006-2952 publication_status: published publisher: Elsevier publist_id: '6782' status: public title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 87 year: '2014' ... --- OA_place: repository OA_type: green _id: '977' abstract: - lang: eng text: We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems. acknowledgement: "We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.\r\n\r\nM. S., M. K., and S. G. contributed equally to this work." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Michael full_name: Knap, Michael last_name: Knap - first_name: Sarang full_name: Gopalakrishnan, Sarang last_name: Gopalakrishnan - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Norman full_name: Yao, Norman last_name: Yao - first_name: Chris full_name: Laumann, Chris last_name: Laumann - first_name: Dmitry full_name: Abanin, Dmitry last_name: Abanin - first_name: Mikhail full_name: Lukin, Mikhail last_name: Lukin - first_name: Eugene full_name: Demler, Eugene last_name: Demler citation: ama: Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204 apa: Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C., … Demler, E. (2014). Interferometric probes of many-body localization. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204 chicago: Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric Probes of Many-Body Localization.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204. ieee: M. Serbyn et al., “Interferometric probes of many-body localization,” Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014. ista: Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin M, Demler E. 2014. Interferometric probes of many-body localization. Physical Review Letters. 113(14). mla: Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.” Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.147204. short: M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin, M. Lukin, E. Demler, Physical Review Letters 113 (2014). date_created: 2018-12-11T11:49:30Z date_published: 2014-10-03T00:00:00Z date_updated: 2026-09-09T10:50:30Z day: '03' doi: 10.1103/PhysRevLett.113.147204 extern: '1' external_id: arxiv: - abs/1403.0693 pmid: - '25325656 ' fulldoi: https://doi.org/10.1103/PhysRevLett.113.147204 intvolume: ' 113' issue: '14' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.0693 month: '10' oa: 1 oa_version: None pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society publist_id: '6421' status: public title: Interferometric probes of many-body localization type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 113 year: '2014' ... --- OA_place: repository OA_type: green _id: '979' abstract: - lang: eng text: In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators. acknowledgement: We thank V. Madhavan and Y. Okada for related collaborations, and P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR 1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0010526. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Liang full_name: Fu, Liang last_name: Fu citation: ama: Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. 2014;90(3). doi:10.1103/PhysRevB.90.035402 apa: Serbyn, M., & Fu, L. (2014). Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.035402 chicago: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.035402. ieee: M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological crystalline insulators,” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 3. American Physical Society, 2014. ista: Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. 90(3). mla: Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 3, American Physical Society, 2014, doi:10.1103/PhysRevB.90.035402. short: M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics 90 (2014). date_created: 2018-12-11T11:49:31Z date_published: 2014-07-03T00:00:00Z date_updated: 2026-09-09T10:53:34Z day: '03' doi: 10.1103/PhysRevB.90.035402 extern: '1' external_id: arxiv: - abs/1403.8153 fulldoi: https://doi.org/10.1103/PhysRevB.90.035402 intvolume: ' 90' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.8153 month: '07' oa: 1 oa_version: None publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - 1098-0121 publication_status: published publisher: American Physical Society publist_id: '6422' status: public title: Symmetry breaking and Landau quantization in topological crystalline insulators type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 90 year: '2014' ... --- OA_type: closed access _id: '926' abstract: - lang: eng text: 'The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.' acknowledgement: We thank Jens Elgeti and Silvia Fre for fruitful discussions. article_processing_charge: No article_type: original author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93). doi:10.1098/rsif.2013.0895 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2013.0895 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” Journal of the Royal Society Interface, vol. 11, no. 93. Royal Society of London, 2014. ista: Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93). mla: Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal Society of London, 2014, doi:10.1098/rsif.2013.0895. short: E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014). date_created: 2018-12-11T11:49:14Z date_published: 2014-04-06T00:00:00Z date_updated: 2026-09-09T11:02:20Z day: '06' doi: 10.1098/rsif.2013.0895 extern: '1' external_id: pmid: - '24478279' fulldoi: https://doi.org/10.1098/rsif.2013.0895 intvolume: ' 11' issue: '93' language: - iso: eng month: '04' oa_version: None pmid: 1 publication: Journal of the Royal Society Interface publication_identifier: eissn: - 1742-5662 issn: - 1742-5689 publication_status: published publisher: Royal Society of London publist_id: '6516' status: public title: Growth homeostatic regulation and stem cell dynamics in tissues type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 11 year: '2014' ... --- OA_type: closed access _id: '925' abstract: - lang: eng text: The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape. acknowledgement: We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D. article_processing_charge: No article_type: original author: - first_name: Bo full_name: Dong, Bo last_name: Dong - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Shigeo full_name: Hayashi, Shigeo last_name: Hayashi citation: ama: Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950. doi:10.1016/j.celrep.2014.03.066 apa: Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066 chicago: Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066. ieee: B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” Cell Reports, vol. 7, no. 4. Cell Press, pp. 941–950, 2014. ista: Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950. mla: Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066. short: B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950. date_created: 2018-12-11T11:49:14Z date_published: 2014-05-22T00:00:00Z date_updated: 2026-09-09T10:59:40Z day: '22' doi: 10.1016/j.celrep.2014.03.066 extern: '1' external_id: pmid: - '24794438 ' fulldoi: https://doi.org/10.1016/j.celrep.2014.03.066 intvolume: ' 7' issue: '4' language: - iso: eng month: '05' oa_version: None page: 941 - 950 pmid: 1 publication: Cell Reports publication_identifier: eissn: - 2211-1247 issn: - 2639-1856 publication_status: published publisher: Cell Press publist_id: '6515' status: public title: Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 7 year: '2014' ... --- OA_type: closed access _id: '927' abstract: - lang: eng text: Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions. article_processing_charge: No article_type: original author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1312076111. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014. ista: Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32. mla: Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:10.1073/pnas.1312076111. short: E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32. date_created: 2018-12-11T11:49:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2026-09-09T11:05:37Z day: '01' doi: 10.1073/pnas.1312076111 extern: '1' external_id: pmid: - '24367079' fulldoi: https://doi.org/10.1073/pnas.1312076111 intvolume: ' 111' issue: '1' language: - iso: eng month: '01' oa_version: None page: 27 - 32 pmid: 1 publication: PNAS publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences publist_id: '6517' status: public title: Theory of epithelial sheet morphology in three dimensions type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 111 year: '2014' ... --- OA_place: publisher OA_type: gold _id: '892' abstract: - lang: eng text: The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution. acknowledgement: "The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.\r\n" article_processing_charge: No article_type: original author: - first_name: Dmitry full_name: Ivankov, Dmitry last_name: Ivankov - first_name: Alexei full_name: Finkelstein, Alexei last_name: Finkelstein - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 2014;26:104-112. doi:10.1016/j.sbi.2014.05.004 apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective of compensatory evolution. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2014.05.004 chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004. ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” Current Opinion in Structural Biology, vol. 26. Elsevier, pp. 104–112, 2014. ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26, 104–112. mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology, vol. 26, Elsevier, 2014, pp. 104–12, doi:10.1016/j.sbi.2014.05.004. short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112. date_created: 2018-12-11T11:49:03Z date_published: 2014-06-01T00:00:00Z date_updated: 2026-09-09T11:10:12Z day: '01' doi: 10.1016/j.sbi.2014.05.004 extern: '1' external_id: pmid: - '24981969' fulldoi: https://doi.org/10.1016/j.sbi.2014.05.004 intvolume: ' 26' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/3.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.sbi.2014.05.004 month: '06' oa: 1 oa_version: None page: 104 - 112 pmid: 1 publication: Current Opinion in Structural Biology publication_identifier: eissn: - 1879-033X issn: - 0959-440X publication_status: published publisher: Elsevier publist_id: '6756' status: public title: A structural perspective of compensatory evolution tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 26 year: '2014' ... --- OA_place: publisher OA_type: gold _id: '863' abstract: - lang: eng text: The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals. acknowledgement: We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22. article_processing_charge: No article_type: original author: - first_name: Leonid full_name: Moroz, Leonid last_name: Moroz - first_name: Kevin full_name: Kocot, Kevin last_name: Kocot - first_name: Mathew full_name: Citarella, Mathew last_name: Citarella - first_name: Sohn full_name: Dosung, Sohn last_name: Dosung - first_name: Tigran full_name: Norekian, Tigran last_name: Norekian - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Anastasia full_name: Grigorenko, Anastasia last_name: Grigorenko - first_name: Christopher full_name: Dailey, Christopher last_name: Dailey - first_name: Eugene full_name: Berezikov, Eugene last_name: Berezikov - first_name: Katherine full_name: Buckley, Katherine last_name: Buckley - first_name: Andrey full_name: Ptitsyn, Andrey last_name: Ptitsyn - first_name: Denis full_name: Reshetov, Denis last_name: Reshetov - first_name: Krishanu full_name: Mukherjee, Krishanu last_name: Mukherjee - first_name: Tatiana full_name: Moroz, Tatiana last_name: Moroz - first_name: Yelena full_name: Bobkova, Yelena last_name: Bobkova - first_name: Fahong full_name: Yu, Fahong last_name: Yu - first_name: Vladimir full_name: Kapitonov, Vladimir last_name: Kapitonov - first_name: Jerzy full_name: Jurka, Jerzy last_name: Jurka - first_name: Yuriy full_name: Bobkov, Yuriy last_name: Bobkov - first_name: Joshua full_name: Swore, Joshua last_name: Swore - first_name: David full_name: Girardo, David last_name: Girardo - first_name: Alexander full_name: Fodor, Alexander last_name: Fodor - first_name: Fedor full_name: Gusev, Fedor last_name: Gusev - first_name: Rachel full_name: Sanford, Rachel last_name: Sanford - first_name: Rebecca full_name: Bruders, Rebecca last_name: Bruders - first_name: Ellen full_name: Kittler, Ellen last_name: Kittler - first_name: Claudia full_name: Mills, Claudia last_name: Mills - first_name: Jonathan full_name: Rast, Jonathan last_name: Rast - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Victor full_name: Solovyev, Victor last_name: Solovyev - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Billie full_name: Swalla, Billie last_name: Swalla - first_name: Jonathan full_name: Sweedler, Jonathan last_name: Sweedler - first_name: Evgeny full_name: Rogaev, Evgeny last_name: Rogaev - first_name: Kenneth full_name: Halanych, Kenneth last_name: Halanych - first_name: Andrea full_name: Kohn, Andrea last_name: Kohn citation: ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400 apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400 chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13400. ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014. ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114. mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:10.1038/nature13400. short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114. date_created: 2018-12-11T11:48:54Z date_published: 2014-01-01T00:00:00Z date_updated: 2026-09-09T11:20:45Z day: '01' doi: 10.1038/nature13400 extern: '1' external_id: pmid: - '24847885' fulldoi: https://doi.org/10.1038/nature13400 intvolume: ' 510' issue: '7503' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '01' oa_version: None page: 109 - 114 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Nature Publishing Group publist_id: '6785' status: public title: The ctenophore genome and the evolutionary origins of neural systems tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 510 year: '2014' ... --- OA_place: publisher OA_type: gold _id: '845' abstract: - lang: eng text: Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena. acknowledgement: The authors are grateful to Georgii Bazykin for valuable discussion and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology for Sanger sequencing. This study was supported by the Russian government grant No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute International Early Career Scientist Award and EMBO Young Investigator Program, and core funds provided by the University of Michigan. article_processing_charge: No article_type: original author: - first_name: Vladimir full_name: Seplyarskiy, Vladimir last_name: Seplyarskiy - first_name: Maria full_name: Logacheva, Maria last_name: Logacheva - first_name: Aleksey full_name: Penin, Aleksey last_name: Penin - first_name: Maria full_name: Baranová, Maria last_name: Baranová - first_name: Evgeny full_name: Leushkin, Evgeny last_name: Leushkin - first_name: Natalia full_name: Demidenko, Natalia last_name: Demidenko - first_name: Anna full_name: Klepikova, Anna last_name: Klepikova - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey last_name: Kondrashov - first_name: Timothy full_name: James, Timothy last_name: James citation: ama: Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242 apa: Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N., … James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu242 chicago: Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242. ieee: V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” Molecular Biology and Evolution, vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014. ista: Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025. mla: Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242. short: V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025. date_created: 2018-12-11T11:48:48Z date_published: 2014-11-01T00:00:00Z date_updated: 2026-09-09T12:19:53Z day: '01' doi: 10.1093/molbev/msu242 extern: '1' external_id: pmid: - '25135947' fulldoi: https://doi.org/10.1093/molbev/msu242 intvolume: ' 31' issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '11' oa_version: None page: 3016 - 3025 pmid: 1 publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press publist_id: '6801' status: public title: Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 31 year: '2014' ... --- OA_place: publisher OA_type: gold _id: '856' abstract: - lang: eng text: The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network. acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.' article_processing_charge: No article_type: original author: - first_name: Ksenia full_name: Pougach, Ksenia last_name: Pougach - first_name: Arnout full_name: Voet, Arnout last_name: Voet - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Karin full_name: Voordeckers, Karin last_name: Voordeckers - first_name: Joaquin full_name: Christiaens, Joaquin last_name: Christiaens - first_name: Bianka full_name: Baying, Bianka last_name: Baying - first_name: Vladimı́R full_name: Bénès, Vladimı́R last_name: Bénès - first_name: Ryo full_name: Sakai, Ryo last_name: Sakai - first_name: Jan full_name: Aerts, Jan last_name: Aerts - first_name: Bo full_name: Zhu, Bo last_name: Zhu - first_name: Patrick full_name: Van Dijck, Patrick last_name: Van Dijck - first_name: Kevin full_name: Verstrepen, Kevin last_name: Verstrepen citation: ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 2014;5. doi:10.1038/ncomms5868 apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms5868 chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868. ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5. mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications, vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868. short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014). date_created: 2018-12-11T11:48:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2026-09-09T12:14:06Z day: '01' doi: 10.1038/ncomms5868 extern: '1' external_id: pmid: - '25204769 ' fulldoi: https://doi.org/10.1038/ncomms5868 intvolume: ' 5' language: - iso: eng month: '01' oa_version: None pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Nature Publishing Group publist_id: '6790' status: public title: Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 5 year: '2014' ... --- OA_place: publisher OA_type: gold _id: '852' abstract: - lang: eng text: 'Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. ' article_processing_charge: No article_type: original author: - first_name: Oriol full_name: Rosello, Oriol last_name: Rosello - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955. doi:10.1093/gbe/evu159 apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evu159 chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159. ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” Genome Biology and Evolution, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014. ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955. mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159. short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955. date_created: 2018-12-11T11:48:51Z date_published: 2014-08-01T00:00:00Z date_updated: 2026-09-09T12:17:30Z day: '01' doi: 10.1093/gbe/evu159 extern: '1' external_id: pmid: - '25070510' fulldoi: https://doi.org/10.1093/gbe/evu159 intvolume: ' 6' issue: '8' language: - iso: eng month: '08' oa_version: None page: 1949 - 1955 pmid: 1 publication: Genome Biology and Evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford University Press publist_id: '6797' status: public title: Long-Term asymmetrical acceleration of protein evolution after gene duplication 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2014' ... --- OA_type: closed access _id: '773' abstract: - lang: eng text: "We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n/2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(n log3n) messages in expectation, which is again within logarithmic factors of optimal.We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt + t2log2t) total messages. Our protocol uses messages of size O(log n), and can therefore scale to large networks.\r\n\r\nWe consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary.\r\n\r\nOur approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model." alternative_title: - LNCS article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Valerie full_name: King, Valerie last_name: King - first_name: Jared full_name: Saia, Jared last_name: Saia citation: ama: 'Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. In: Kuhn F, ed. 28th International Symposium Distributed Computing 2014. Vol 8784. Springer; 2014:61-75. doi:10.1007/978-3-662-45174-8_5' apa: 'Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2014). Communication-efficient randomized consensus. In F. Kuhn (Ed.), 28th International Symposium Distributed Computing 2014 (Vol. 8784, pp. 61–75). Austin, TX, United States: Springer. https://doi.org/10.1007/978-3-662-45174-8_5' chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” In 28th International Symposium Distributed Computing 2014, edited by Fabian Kuhn, 8784:61–75. Springer, 2014. https://doi.org/10.1007/978-3-662-45174-8_5. ieee: D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” in 28th International Symposium Distributed Computing 2014, Austin, TX, United States, 2014, vol. 8784, pp. 61–75. ista: 'Alistarh D-A, Aspnes J, King V, Saia J. 2014. Communication-efficient randomized consensus. 28th International Symposium Distributed Computing 2014. DISC: Distributed Computing, LNCS, vol. 8784, 61–75.' mla: Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” 28th International Symposium Distributed Computing 2014, edited by Fabian Kuhn, vol. 8784, Springer, 2014, pp. 61–75, doi:10.1007/978-3-662-45174-8_5. short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, in:, F. Kuhn (Ed.), 28th International Symposium Distributed Computing 2014, Springer, 2014, pp. 61–75. conference: end_date: 2014-10-15 location: Austin, TX, United States name: 'DISC: Distributed Computing' start_date: 2014-10-12 date_created: 2018-12-11T11:48:25Z date_published: 2014-01-01T00:00:00Z date_updated: 2026-09-09T12:28:14Z day: '01' doi: 10.1007/978-3-662-45174-8_5 editor: - first_name: Fabian full_name: Kuhn, Fabian last_name: Kuhn extern: '1' fulldoi: https://doi.org/10.1007/978-3-662-45174-8_5 intvolume: ' 8784' language: - iso: eng month: '01' oa_version: None page: 61 - 75 publication: 28th International Symposium Distributed Computing 2014 publication_identifier: eisbn: - '9783662451748' isbn: - '9783662451731' publication_status: published publisher: Springer publist_id: '6881' status: public title: Communication-efficient randomized consensus type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 8784 year: '2014' ... --- OA_place: repository OA_type: green _id: '775' abstract: - lang: eng text: 'The long-lived renaming problem appears in shared-memory systems where a set of threads need to register and deregister frequently from the computation, while concurrent operations scan the set of currently registered threads. Instances of this problem show up in concurrent implementations of transactional memory, flat combining, thread barriers, and memory reclamation schemes for lock-free data structures. In this paper, we analyze a randomized solution for long-lived renaming. The algorithmic technique we consider, called the Level Array, has previously been used for hashing and one-shot (single-use) renaming. Our main contribution is to prove that, in long-lived executions, where processes may register and deregister polynomially many times, the technique guarantees constant steps on average and O (log log n) steps with high probability for registering, unit cost for deregistering, and O (n) steps for collect queries, where n is an upper bound on the number of processes that may be active at any point in time. We also show that the algorithm has the surprising property that it is self-healing: under reasonable assumptions on the schedule, operations running while the data structure is in a degraded state implicitly help the data structure re-balance itself. This subtle mechanism obviates the need for expensive periodic rebuilding procedures. Our benchmarks validate this approach, showing that, for typical use parameters, the average number of steps a process takes to register is less than two and the worst-case number of steps is bounded by six, even in executions with billions of operations. We contrast this with other randomized implementations, whose worst-case behavior we show to be unreliable, and with deterministic implementations, whose cost is linear in n.' article_processing_charge: No arxiv: 1 author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. The levelarray: A fast, practical long-lived renaming algorithm. In: Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems. IEEE; 2014:348-357. doi:10.1109/ICDCS.2014.43' apa: 'Alistarh, D.-A., Kopinsky, J., Matveev, A., & Shavit, N. (2014). The levelarray: A fast, practical long-lived renaming algorithm. In Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems (pp. 348–357). Madrid, Spain: IEEE. https://doi.org/10.1109/ICDCS.2014.43' chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Alexander Matveev, and Nir Shavit. “The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm.” In Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems, 348–57. IEEE, 2014. https://doi.org/10.1109/ICDCS.2014.43.' ieee: 'D.-A. Alistarh, J. Kopinsky, A. Matveev, and N. Shavit, “The levelarray: A fast, practical long-lived renaming algorithm,” in Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems, Madrid, Spain, 2014, pp. 348–357.' ista: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. 2014. The levelarray: A fast, practical long-lived renaming algorithm. Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems, 348–357.' mla: 'Alistarh, Dan-Adrian, et al. “The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm.” Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems, IEEE, 2014, pp. 348–57, doi:10.1109/ICDCS.2014.43.' short: D.-A. Alistarh, J. Kopinsky, A. Matveev, N. Shavit, in:, Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems, IEEE, 2014, pp. 348–357. conference: end_date: 2014-07-03 location: Madrid, Spain name: 'ICDCS: International Conference on Distributed Computing Systems' start_date: 2014-06-30 date_created: 2018-12-11T11:48:26Z date_published: 2014-08-29T00:00:00Z date_updated: 2026-09-09T12:34:00Z day: '29' doi: 10.1109/ICDCS.2014.43 extern: '1' external_id: arxiv: - '1405.5461' fulldoi: https://doi.org/10.1109/ICDCS.2014.43 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1405.5461 month: '08' oa: 1 oa_version: Preprint page: 348 - 357 publication: Proceedings of the 2014 IEEE 34th International Conference on Distributed Computing Systems publication_identifier: eisbn: - '9781479951697' issn: - 1063-6927 publication_status: published publisher: IEEE publist_id: '6883' status: public title: 'The levelarray: A fast, practical long-lived renaming algorithm' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2014' ...