--- _id: '1442' abstract: - lang: eng text: We give a cohomological interpretation of both the Kac polynomial and the refined Donaldson-Thomas-invariants of quivers. This interpretation yields a proof of a conjecture of Kac from 1982 and gives a new perspective on recent work of Kontsevich-Soibelman. Thisis achieved by computing, via an arithmetic Fourier transform, the dimensions of the isotypical components of the cohomology of associated Nakajima quiver varieties under the action of a Weyl group. The generating function of the corresponding Poincare polynomials is an extension of Hua's formula for Kac polynomials of quivers involving Hall-Littlewood symmetric functions. The resulting formulae contain a wide range of information on the geometry of the quiver varieties. acknowledgement: |- The first author thanks the Royal Society for funding his research 2005-2012 in the form of a Royal Society University Research Fellowship as well as the Mathematical Institute and Wadham College in Oxford for a very productive environment. The second author is supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01. The third author is supported by the NSF grant DMS-1101484 and a Research Scholarship from the Clay Mathematical Institute. author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Emmanuel full_name: Letellier, Emmanuel last_name: Letellier - first_name: Fernando full_name: Rodríguez Villegas, Fernando last_name: Rodríguez Villegas citation: ama: Hausel T, Letellier E, Rodríguez Villegas F. Positivity for Kac polynomials and DT-invariants of quivers. Annals of Mathematics. 2013;177(3):1147-1168. doi:10.4007/annals.2013.177.3.8 apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2013). Positivity for Kac polynomials and DT-invariants of quivers. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2013.177.3.8 chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Positivity for Kac Polynomials and DT-Invariants of Quivers.” Annals of Mathematics. Princeton University Press, 2013. https://doi.org/10.4007/annals.2013.177.3.8. ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Positivity for Kac polynomials and DT-invariants of quivers,” Annals of Mathematics, vol. 177, no. 3. Princeton University Press, pp. 1147–1168, 2013. ista: Hausel T, Letellier E, Rodríguez Villegas F. 2013. Positivity for Kac polynomials and DT-invariants of quivers. Annals of Mathematics. 177(3), 1147–1168. mla: Hausel, Tamás, et al. “Positivity for Kac Polynomials and DT-Invariants of Quivers.” Annals of Mathematics, vol. 177, no. 3, Princeton University Press, 2013, pp. 1147–68, doi:10.4007/annals.2013.177.3.8. short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Annals of Mathematics 177 (2013) 1147–1168. date_created: 2018-12-11T11:52:02Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:50:47Z day: '01' doi: 10.4007/annals.2013.177.3.8 extern: 1 intvolume: ' 177' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1204.2375 month: '01' oa: 1 page: 1147 - 1168 publication: Annals of Mathematics publication_status: published publisher: Princeton University Press publist_id: '5754' quality_controlled: 0 status: public title: Positivity for Kac polynomials and DT-invariants of quivers type: journal_article volume: 177 year: '2013' ... --- _id: '1443' abstract: - lang: eng text: 'Here we survey several results and conjectures on the cohomology of the total space of the Hitchin system: the moduli space of semi-stable rank n and degree d Higgs bundles on a complex algebraic curve C. The picture emerging is a dynamic mixture of ideas originating in theoretical physics such as gauge theory and mirror symmetry, Weil conjectures in arithmetic algebraic geometry, representation theory of finite groups of Lie type and Langlands duality in number theory.' alternative_title: - Advanced Lectures in Mathematics author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel citation: ama: 'Hausel T. Global topology of the Hitchin system. In: Handbook of Moduli: Volume II. Vol 25. International Press; 2013:29-70.' apa: 'Hausel, T. (2013). Global topology of the Hitchin system. In Handbook of Moduli: Volume II (Vol. 25, pp. 29–70). International Press.' chicago: 'Hausel, Tamás. “Global Topology of the Hitchin System.” In Handbook of Moduli: Volume II, 25:29–70. International Press, 2013.' ieee: 'T. Hausel, “Global topology of the Hitchin system,” in Handbook of Moduli: Volume II, vol. 25, International Press, 2013, pp. 29–70.' ista: 'Hausel T. 2013.Global topology of the Hitchin system. In: Handbook of Moduli: Volume II. Advanced Lectures in Mathematics, vol. 25, 29–70.' mla: 'Hausel, Tamás. “Global Topology of the Hitchin System.” Handbook of Moduli: Volume II, vol. 25, International Press, 2013, pp. 29–70.' short: 'T. Hausel, in:, Handbook of Moduli: Volume II, International Press, 2013, pp. 29–70.' date_created: 2018-12-11T11:52:03Z date_published: 2013-03-15T00:00:00Z date_updated: 2021-01-12T06:50:47Z day: '15' extern: 1 intvolume: ' 25' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1102.1717 month: '03' oa: 1 page: 29 - 70 publication: 'Handbook of Moduli: Volume II' publication_status: published publisher: International Press publist_id: '5753' quality_controlled: 0 status: public title: Global topology of the Hitchin system type: book_chapter volume: 25 year: '2013' ... --- _id: '1469' abstract: - lang: eng text: We study connections between the topology of generic character varieties of fundamental groups of punctured Riemann surfaces, Macdonald polynomials, quiver representations, Hilbert schemes on Cx × Cx, modular forms and multiplicities in tensor products of irreducible characters of finite general linear groups. acknowledgement: During the preparation of this paper TH was supported by a Royal Society University Research Fellowship at the University of Oxford. EL was supported by ANR-09-JCJC-0102-01. FRV was supported by NSF grant DMS-0200605, an FRA from the University of Texas at Austin, EPSRC grant EP/G027110/1, Visiting Fellowships at All Souls and Wadham Colleges in Oxford and a Research Scholarship from the Clay Mathematical Institute. author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Emmanuel full_name: Letellier, Emmanuel last_name: Letellier - first_name: Fernando full_name: Rodríguez Villegas, Fernando last_name: Rodríguez Villegas citation: ama: Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. 2013;234:85-128. doi:10.1016/j.aim.2012.10.009 apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2013). Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2012.10.009 chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties II.” Advances in Mathematics. Academic Press, 2013. https://doi.org/10.1016/j.aim.2012.10.009. ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties II,” Advances in Mathematics, vol. 234. Academic Press, pp. 85–128, 2013. ista: Hausel T, Letellier E, Rodríguez Villegas F. 2013. Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. 234, 85–128. mla: Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties II.” Advances in Mathematics, vol. 234, Academic Press, 2013, pp. 85–128, doi:10.1016/j.aim.2012.10.009. short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Advances in Mathematics 234 (2013) 85–128. date_created: 2018-12-11T11:52:12Z date_published: 2013-02-15T00:00:00Z date_updated: 2021-01-12T06:50:57Z day: '15' doi: 10.1016/j.aim.2012.10.009 extern: 1 intvolume: ' 234' month: '02' page: 85 - 128 publication: Advances in Mathematics publication_status: published publisher: Academic Press publist_id: '5724' quality_controlled: 0 status: public title: Arithmetic harmonic analysis on character and quiver varieties II type: journal_article volume: 234 year: '2013' ... --- _id: '1470' abstract: - lang: eng text: We show that a natural isomorphism between the rational cohomology groups of the two zero-dimensional Hilbert schemes of n-points of two surfaces, the affine plane minus the axes and the cotangent bundle of an elliptic curve, exchanges the weight filtration on the first set of cohomology groups with the perverse Leray filtration associated with a natural fibration on the second set of cohomology groups. We discuss some associated hard Lefschetz phenomena. acknowledgement: Mark Andrea A. de Cataldo was partially supported by N.S.A. and N.S.F. Tamás Hausel was supported by a Royal Society University Research Fellowship. Luca Migliorini was partially supported by PRIN 2007 project "Spazi di moduli e teoria di Lie" author: - first_name: Mark full_name: De Cataldo, Mark A last_name: De Cataldo - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Luca full_name: Migliorini, Luca last_name: Migliorini citation: ama: De Cataldo M, Hausel T, Migliorini L. Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. Journal of Singularities. 2013;7:23-38. doi:10.5427/jsing.2013.7c apa: De Cataldo, M., Hausel, T., & Migliorini, L. (2013). Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. Journal of Singularities. Worldwide Center of Mathematics. https://doi.org/10.5427/jsing.2013.7c chicago: De Cataldo, Mark, Tamás Hausel, and Luca Migliorini. “Exchange between Perverse and Weight Filtration for the Hilbert Schemes of Points of Two Surfaces.” Journal of Singularities. Worldwide Center of Mathematics, 2013. https://doi.org/10.5427/jsing.2013.7c. ieee: M. De Cataldo, T. Hausel, and L. Migliorini, “Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces,” Journal of Singularities, vol. 7. Worldwide Center of Mathematics, pp. 23–38, 2013. ista: De Cataldo M, Hausel T, Migliorini L. 2013. Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. Journal of Singularities. 7, 23–38. mla: De Cataldo, Mark, et al. “Exchange between Perverse and Weight Filtration for the Hilbert Schemes of Points of Two Surfaces.” Journal of Singularities, vol. 7, Worldwide Center of Mathematics, 2013, pp. 23–38, doi:10.5427/jsing.2013.7c. short: M. De Cataldo, T. Hausel, L. Migliorini, Journal of Singularities 7 (2013) 23–38. date_created: 2018-12-11T11:52:12Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:50:58Z day: '01' doi: 10.5427/jsing.2013.7c extern: 1 intvolume: ' 7' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1012.2583 month: '01' oa: 1 page: 23 - 38 publication: Journal of Singularities publication_status: published publisher: Worldwide Center of Mathematics publist_id: '5725' quality_controlled: 0 status: public title: Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces type: journal_article volume: 7 year: '2013' ... --- _id: '11758' article_processing_charge: No article_type: letter_note author: - first_name: Luca full_name: Aceto, Luca last_name: Aceto - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Jiří full_name: Sgall, Jiří last_name: Sgall citation: ama: Aceto L, Henzinger MH, Sgall J. 38th International Colloquium on Automata, Languages and Programming. Information and Computation. 2013;222(1):1. doi:10.1016/j.ic.2012.11.002 apa: Aceto, L., Henzinger, M. H., & Sgall, J. (2013). 38th International Colloquium on Automata, Languages and Programming. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2012.11.002 chicago: Aceto, Luca, Monika H Henzinger, and Jiří Sgall. “38th International Colloquium on Automata, Languages and Programming.” Information and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2012.11.002. ieee: L. Aceto, M. H. Henzinger, and J. Sgall, “38th International Colloquium on Automata, Languages and Programming,” Information and Computation, vol. 222, no. 1. Elsevier, p. 1, 2013. ista: Aceto L, Henzinger MH, Sgall J. 2013. 38th International Colloquium on Automata, Languages and Programming. Information and Computation. 222(1), 1. mla: Aceto, Luca, et al. “38th International Colloquium on Automata, Languages and Programming.” Information and Computation, vol. 222, no. 1, Elsevier, 2013, p. 1, doi:10.1016/j.ic.2012.11.002. short: L. Aceto, M.H. Henzinger, J. Sgall, Information and Computation 222 (2013) 1. date_created: 2022-08-08T11:25:34Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-23T10:09:19Z day: '01' doi: 10.1016/j.ic.2012.11.002 extern: '1' intvolume: ' 222' issue: '1' language: - iso: eng month: '01' oa_version: None page: '1' publication: Information and Computation publication_identifier: issn: - 0890-5401 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 38th International Colloquium on Automata, Languages and Programming type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 222 year: '2013' ... --- _id: '1726' abstract: - lang: eng text: The development of a functional tissue requires coordination of the amplification of progenitors and their differentiation into specific cell types. The molecular basis for this coordination during myotome ontogeny is not well understood. Dermomytome progenitors that colonize the myotome first acquire myocyte identity and subsequently proliferate as Pax7-expressing progenitors before undergoing terminal differentiation. We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this transition in both avian and mouse embryos. Initially, Shh ligand emanating from notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation of dermomyotome cells and promotes myogenic differentiation of progenitors that colonized the myotome. Interfering with Shh signaling at this stage produces small myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter of Shh activity combined with mouse genetics revealed the existence of both activator and repressor Shh activities operating on distinct subsets of cells during the epaxial myotomal maturation. In contrast to observations in mice, in avians Shh promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently, myogenic progenitors become refractory to Shh; this is likely to occur at the level of, or upstream of, smoothened signaling. The end of responsiveness to Shh coincides with, and is thus likely to enable, the transition into the growth phase of the myotome. acknowledgement: This study was supported by grants from the Israel Science Foundation (ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642 to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release after 6 months author: - first_name: Nitza full_name: Kahane, Nitza last_name: Kahane - first_name: Vanessa full_name: Ribes, Vanessa last_name: Ribes - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Chaya full_name: Kalcheim, Chaya last_name: Kalcheim citation: ama: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. 2013;140(8):1740-1750. doi:10.1242/dev.092726 apa: Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., & Kalcheim, C. (2013). The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. Company of Biologists. https://doi.org/10.1242/dev.092726 chicago: Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.092726. ieee: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling,” Development, vol. 140, no. 8. Company of Biologists, pp. 1740–1750, 2013. ista: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750. mla: Kahane, Nitza, et al. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” Development, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50, doi:10.1242/dev.092726. short: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140 (2013) 1740–1750. date_created: 2018-12-11T11:53:41Z date_published: 2013-04-18T00:00:00Z date_updated: 2021-01-12T06:52:47Z day: '18' doi: 10.1242/dev.092726 extern: 1 intvolume: ' 140' issue: '8' month: '04' page: 1740 - 1750 publication: Development publication_status: published publisher: Company of Biologists publist_id: '5402' quality_controlled: 0 status: public title: The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling type: journal_article volume: 140 year: '2013' ... --- _id: '1727' abstract: - lang: eng text: 'Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking.' author: - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Laurent full_name: Holtzer, Laurent last_name: Holtzer - first_name: Ortrud full_name: Wartlick, Ortrud last_name: Wartlick - first_name: Thomas full_name: Schmidt, Thomas S last_name: Schmidt - first_name: Marcos full_name: González-Gaitán, Marcos A last_name: González Gaitán citation: ama: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. 2013;8(5):387-403. doi:10.1101/pdb.top074237 apa: Kicheva, A., Holtzer, L., Wartlick, O., Schmidt, T., & González Gaitán, M. (2013). Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/pdb.top074237 chicago: Kicheva, Anna, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt, and Marcos González Gaitán. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press, 2013. https://doi.org/10.1101/pdb.top074237. ieee: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, and M. González Gaitán, “Quantitative imaging of morphogen gradients in drosophila imaginal discs,” Cold Spring Harbor Protocols, vol. 8, no. 5. Cold Spring Harbor Laboratory Press, pp. 387–403, 2013. ista: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. 2013. Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. 8(5), 387–403. mla: Kicheva, Anna, et al. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” Cold Spring Harbor Protocols, vol. 8, no. 5, Cold Spring Harbor Laboratory Press, 2013, pp. 387–403, doi:10.1101/pdb.top074237. short: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold Spring Harbor Protocols 8 (2013) 387–403. date_created: 2018-12-11T11:53:41Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:52:47Z day: '01' doi: 10.1101/pdb.top074237 extern: 1 intvolume: ' 8' issue: '5' month: '05' page: 387 - 403 publication: Cold Spring Harbor Protocols publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '5401' quality_controlled: 0 status: public title: Quantitative imaging of morphogen gradients in drosophila imaginal discs type: journal_article volume: 8 year: '2013' ... --- _id: '1760' abstract: - lang: eng text: We report on hole g-factor measurements in three terminal SiGe self-assembled quantum dot devices with a top gate electrode positioned very close to the nanostructure. Measurements of both the perpendicular as well as the parallel g-factor reveal significant changes for a small modulation of the top gate voltage. From the observed modulations, we estimate that, for realistic experimental conditions, hole spins can be electrically manipulated with Rabi frequencies in the order of 100 MHz. This work emphasises the potential of hole-based nano-devices for efficient spin manipulation by means of the g-tensor modulation technique. acknowledgement: We acknowledge the financial support from the Nanosciences Foundation (Grenoble, France), the Commission for a Marie Curie Carrer Integration Grant, the Austrian Science Fund (FWF) for a Lise-Meitner Fellowship (M1435-N30), the DOE under Contract No. DE-FG02-08ER46482 (Yale), the European Starting Grant program, and the Agence Nationale de la Recherche author: - first_name: Natalia full_name: Ares, Natalia last_name: Ares - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Vitaly full_name: Golovach, Vitaly N last_name: Golovach - first_name: Jianjun full_name: Zhang, Jianjun last_name: Zhang - first_name: Aaron full_name: Prager, Aaron A last_name: Prager - first_name: Leonid full_name: Glazman, Leonid I last_name: Glazman - first_name: Oliver full_name: Schmidt, Oliver G last_name: Schmidt - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Ares N, Katsaros G, Golovach V, et al. SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. 2013;103(26). doi:10.1063/1.4858959 apa: Ares, N., Katsaros, G., Golovach, V., Zhang, J., Prager, A., Glazman, L., … De Franceschi, S. (2013). SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.4858959 chicago: Ares, Natalia, Georgios Katsaros, Vitaly Golovach, Jianjun Zhang, Aaron Prager, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” Applied Physics Letters. American Institute of Physics, 2013. https://doi.org/10.1063/1.4858959. ieee: N. Ares et al., “SiGe quantum dots for fast hole spin Rabi oscillations,” Applied Physics Letters, vol. 103, no. 26. American Institute of Physics, 2013. ista: Ares N, Katsaros G, Golovach V, Zhang J, Prager A, Glazman L, Schmidt O, De Franceschi S. 2013. SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. 103(26). mla: Ares, Natalia, et al. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” Applied Physics Letters, vol. 103, no. 26, American Institute of Physics, 2013, doi:10.1063/1.4858959. short: N. Ares, G. Katsaros, V. Golovach, J. Zhang, A. Prager, L. Glazman, O. Schmidt, S. De Franceschi, Applied Physics Letters 103 (2013). date_created: 2018-12-11T11:53:52Z date_published: 2013-01-23T00:00:00Z date_updated: 2021-01-12T06:53:02Z day: '23' doi: 10.1063/1.4858959 extern: 1 intvolume: ' 103' issue: '26' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.7196 month: '01' oa: 1 publication: Applied Physics Letters publication_status: published publisher: American Institute of Physics publist_id: '5364' quality_controlled: 0 status: public title: SiGe quantum dots for fast hole spin Rabi oscillations type: journal_article volume: 103 year: '2013' ... --- _id: '1759' abstract: - lang: eng text: We report an electric-field-induced giant modulation of the hole g factor in SiGe nanocrystals. The observed effect is ascribed to a so-far overlooked contribution to the g factor that stems from the mixing between heavy- and light-hole wave functions. We show that the relative displacement between the confined heavy- and light-hole states, occurring upon application of the electric field, alters their mixing strength leading to a strong nonmonotonic modulation of the g factor. acknowledgement: We acknowledge financial support from the Nanosciences Foundation (Grenoble, France), DOE under Contract No. DEFG02-08ER46482 (Yale), the Agence Nationale de la Recherche, and the European Starting Grant. G. K. acknowledges support from the European Commission via a Marie Curie Carrer Integration Grant and the FWF for a Lise-Meitner Fellowship author: - first_name: Natalia full_name: Ares, Natalia last_name: Ares - first_name: Vitaly full_name: Golovach, Vitaly N last_name: Golovach - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Mathieu full_name: Stoffel, Mathieu last_name: Stoffel - first_name: Frank full_name: Fournel, Frank last_name: Fournel - first_name: Leonid full_name: Glazman, Leonid I last_name: Glazman - first_name: Oliver full_name: Schmidt, Oliver G last_name: Schmidt - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Ares N, Golovach V, Katsaros G, et al. Nature of tunable hole g factors in quantum dots. Physical Review Letters. 2013;110(4). doi:10.1103/PhysRevLett.110.046602 apa: Ares, N., Golovach, V., Katsaros, G., Stoffel, M., Fournel, F., Glazman, L., … De Franceschi, S. (2013). Nature of tunable hole g factors in quantum dots. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.046602 chicago: Ares, Natalia, Vitaly Golovach, Georgios Katsaros, Mathieu Stoffel, Frank Fournel, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “Nature of Tunable Hole g Factors in Quantum Dots.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.046602. ieee: N. Ares et al., “Nature of tunable hole g factors in quantum dots,” Physical Review Letters, vol. 110, no. 4. American Physical Society, 2013. ista: Ares N, Golovach V, Katsaros G, Stoffel M, Fournel F, Glazman L, Schmidt O, De Franceschi S. 2013. Nature of tunable hole g factors in quantum dots. Physical Review Letters. 110(4). mla: Ares, Natalia, et al. “Nature of Tunable Hole g Factors in Quantum Dots.” Physical Review Letters, vol. 110, no. 4, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.046602. short: N. Ares, V. Golovach, G. Katsaros, M. Stoffel, F. Fournel, L. Glazman, O. Schmidt, S. De Franceschi, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:53:51Z date_published: 2013-01-23T00:00:00Z date_updated: 2021-01-12T06:53:01Z day: '23' doi: 10.1103/PhysRevLett.110.046602 extern: 1 intvolume: ' 110' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1208.0476 month: '01' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5365' quality_controlled: 0 status: public title: Nature of tunable hole g factors in quantum dots type: journal_article volume: 110 year: '2013' ... --- _id: '1785' abstract: - lang: eng text: The geometric aspects of quantum mechanics are emphasized most prominently by the concept of geometric phases, which are acquired whenever a quantum system evolves along a path in Hilbert space, that is, the space of quantum states of the system. The geometric phase is determined only by the shape of this path and is, in its simplest form, a real number. However, if the system has degenerate energy levels, then matrix-valued geometric state transformations, known as non-Abelian holonomies-the effect of which depends on the order of two consecutive paths-can be obtained. They are important, for example, for the creation of synthetic gauge fields in cold atomic gases or the description of non-Abelian anyon statistics. Moreover, there are proposals to exploit non-Abelian holonomic gates for the purposes of noise-resilient quantum computation. In contrast to Abelian geometric operations, non-Abelian ones have been observed only in nuclear quadrupole resonance experiments with a large number of spins, and without full characterization of the geometric process and its non-commutative nature. Here we realize non-Abelian non-adiabatic holonomic quantum operations on a single, superconducting, artificial three-level atom by applying a well-controlled, two-tone microwave drive. Using quantum process tomography, we determine fidelities of the resulting non-commuting gates that exceed 95 per cent. We show that two different quantum gates, originating from two distinct paths in Hilbert space, yield non-equivalent transformations when applied in different orders. This provides evidence for the non-Abelian character of the implemented holonomic quantum operations. In combination with a non-trivial two-quantum-bit gate, our method suggests a way to universal holonomic quantum computing. acknowledgement: This work is supported financially by GEOMDISS, the Swiss National Science Foundation and ETH Zurich author: - first_name: Abdufarrukh full_name: Abdumalikov, Abdufarrukh A last_name: Abdumalikov - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: K full_name: Juliusson, K last_name: Juliusson - first_name: M full_name: Pechal, M last_name: Pechal - first_name: Stefan full_name: Berger, Stefan T last_name: Berger - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp citation: ama: Abdumalikov A, Fink JM, Juliusson K, et al. Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. 2013;496(7446):482-485. doi:10.1038/nature12010 apa: Abdumalikov, A., Fink, J. M., Juliusson, K., Pechal, M., Berger, S., Wallraff, A., & Filipp, S. (2013). Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12010 chicago: Abdumalikov, Abdufarrukh, Johannes M Fink, K Juliusson, M Pechal, Stefan Berger, Andreas Wallraff, and Stefan Filipp. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12010. ieee: A. Abdumalikov et al., “Experimental realization of non-Abelian non-adiabatic geometric gates,” Nature, vol. 496, no. 7446. Nature Publishing Group, pp. 482–485, 2013. ista: Abdumalikov A, Fink JM, Juliusson K, Pechal M, Berger S, Wallraff A, Filipp S. 2013. Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. 496(7446), 482–485. mla: Abdumalikov, Abdufarrukh, et al. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” Nature, vol. 496, no. 7446, Nature Publishing Group, 2013, pp. 482–85, doi:10.1038/nature12010. short: A. Abdumalikov, J.M. Fink, K. Juliusson, M. Pechal, S. Berger, A. Wallraff, S. Filipp, Nature 496 (2013) 482–485. date_created: 2018-12-11T11:54:00Z date_published: 2013-04-25T00:00:00Z date_updated: 2021-01-12T06:53:11Z day: '25' doi: 10.1038/nature12010 extern: 1 intvolume: ' 496' issue: '7446' month: '04' page: 482 - 485 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5329' quality_controlled: 0 status: public title: Experimental realization of non-Abelian non-adiabatic geometric gates type: journal_article volume: 496 year: '2013' ... --- _id: '1787' abstract: - lang: eng text: When two indistinguishable single photons impinge at the two inputs of a beam splitter they coalesce into a pair of photons appearing in either one of its two outputs. This effect is due to the bosonic nature of photons and was first experimentally observed by Hong, Ou and Mandel. Here, we present the observation of the Hong-Ou-Mandel effect with two independent single-photon sources in the microwave frequency domain. We probe the indistinguishability of single photons, created with a controllable delay, in time-resolved second-order cross- and auto-correlation function measurements. Using quadrature amplitude detection we are able to resolve different photon numbers and detect coherence in and between the output arms. This scheme allows us to fully characterize the two-mode entanglement of the spatially separated beam-splitter output modes. Our experiments constitute a first step towards using two-photon interference at microwave frequencies for quantum communication and information processing. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ. L.S. was supported by EU IP SOLID. A.B. and M.J.W. were supported by NSERC, CIFAR and the Alfred P. Sloan Foundation author: - first_name: C full_name: Lang, C last_name: Lang - first_name: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Matthew full_name: Woolley, Matthew J last_name: Woolley - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Lang C, Eichler C, Steffen L, et al. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. 2013;9(6):345-348. doi:10.1038/nphys2612 apa: Lang, C., Eichler, C., Steffen, L., Fink, J. M., Woolley, M., Blais, A., & Wallraff, A. (2013). Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys2612 chicago: Lang, C, Christopher Eichler, L. Steffen, Johannes M Fink, Matthew Woolley, Alexandre Blais, and Andreas Wallraff. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” Nature Physics. Nature Publishing Group, 2013. https://doi.org/10.1038/nphys2612. ieee: C. Lang et al., “Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies,” Nature Physics, vol. 9, no. 6. Nature Publishing Group, pp. 345–348, 2013. ista: Lang C, Eichler C, Steffen L, Fink JM, Woolley M, Blais A, Wallraff A. 2013. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. 9(6), 345–348. mla: Lang, C., et al. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” Nature Physics, vol. 9, no. 6, Nature Publishing Group, 2013, pp. 345–48, doi:10.1038/nphys2612. short: C. Lang, C. Eichler, L. Steffen, J.M. Fink, M. Woolley, A. Blais, A. Wallraff, Nature Physics 9 (2013) 345–348. date_created: 2018-12-11T11:54:00Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T06:53:11Z day: '01' doi: 10.1038/nphys2612 extern: 1 intvolume: ' 9' issue: '6' month: '06' page: 345 - 348 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '5327' quality_controlled: 0 status: public title: Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies type: journal_article volume: 9 year: '2013' ... --- _id: '1786' abstract: - lang: eng text: We report the experimental observation and a theoretical explanation of collective suppression of linewidths for multiple superconducting qubits coupled to a good cavity. This demonstrates how strong qubit-cavity coupling can significantly modify the dephasing and dissipation processes that might be expected for individual qubits, and can potentially improve coherence times in many-body circuit QED. acknowledgement: J. K. acknowledges financial support from EPSRC program “TOPNES” (EP/I031014/1) and EPSRC (EP/G004714/2) author: - first_name: Felix full_name: Nissen, Felix last_name: Nissen - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Jonas full_name: Mlynek, Jonas A last_name: Mlynek - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Jonathan full_name: Keeling, Jonathan M last_name: Keeling citation: ama: Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. Collective suppression of linewidths in circuit QED. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.203602 apa: Nissen, F., Fink, J. M., Mlynek, J., Wallraff, A., & Keeling, J. (2013). Collective suppression of linewidths in circuit QED. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.203602 chicago: Nissen, Felix, Johannes M Fink, Jonas Mlynek, Andreas Wallraff, and Jonathan Keeling. “Collective Suppression of Linewidths in Circuit QED.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.203602. ieee: F. Nissen, J. M. Fink, J. Mlynek, A. Wallraff, and J. Keeling, “Collective suppression of linewidths in circuit QED,” Physical Review Letters, vol. 110, no. 20. American Physical Society, 2013. ista: Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. 2013. Collective suppression of linewidths in circuit QED. Physical Review Letters. 110(20). mla: Nissen, Felix, et al. “Collective Suppression of Linewidths in Circuit QED.” Physical Review Letters, vol. 110, no. 20, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.203602. short: F. Nissen, J.M. Fink, J. Mlynek, A. Wallraff, J. Keeling, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:54:00Z date_published: 2013-05-15T00:00:00Z date_updated: 2021-01-12T06:53:11Z day: '15' doi: 10.1103/PhysRevLett.110.203602 extern: 1 intvolume: ' 110' issue: '20' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1302.0665 month: '05' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5328' quality_controlled: 0 status: public title: Collective suppression of linewidths in circuit QED type: journal_article volume: 110 year: '2013' ... --- _id: '1790' abstract: - lang: eng text: In the September 12, 2013 issue of Nature, the Epi4K Consortium (. Allen etal., 2013) reported sequencing 264patient trios with epileptic encephalopathies. The Consortium focused on genes exceptionally intolerant to sequence variations and found substantial interconnections with autism and intellectual disability gene networks. author: - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Seungtae full_name: Baek, SeungTae last_name: Baek - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: 'Novarino G, Baek S, Gleeson J. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 2013;80(1):9-11. doi:10.1016/j.neuron.2013.09.019' apa: 'Novarino, G., Baek, S., & Gleeson, J. (2013). The sacred disease: The puzzling genetics of epileptic disorders. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.019' chicago: 'Novarino, Gaia, Seungtae Baek, and Joseph Gleeson. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.09.019.' ieee: 'G. Novarino, S. Baek, and J. Gleeson, “The sacred disease: The puzzling genetics of epileptic disorders,” Neuron, vol. 80, no. 1. Elsevier, pp. 9–11, 2013.' ista: 'Novarino G, Baek S, Gleeson J. 2013. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 80(1), 9–11.' mla: 'Novarino, Gaia, et al. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” Neuron, vol. 80, no. 1, Elsevier, 2013, pp. 9–11, doi:10.1016/j.neuron.2013.09.019.' short: G. Novarino, S. Baek, J. Gleeson, Neuron 80 (2013) 9–11. date_created: 2018-12-11T11:54:01Z date_published: 2013-10-02T00:00:00Z date_updated: 2021-01-12T06:53:13Z day: '02' doi: 10.1016/j.neuron.2013.09.019 extern: 1 intvolume: ' 80' issue: '1' month: '10' page: 9 - 11 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5323' quality_controlled: 0 status: public title: 'The sacred disease: The puzzling genetics of epileptic disorders' type: journal_article volume: 80 year: '2013' ... --- _id: '1977' abstract: - lang: eng text: Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review. acknowledgement: This work was funded by the Medical Research Council. author: - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Rozbeh full_name: 'Baradaran, Rozbeh ' last_name: Baradaran - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: John full_name: Berrisford, John M last_name: Berrisford - first_name: Gurdeep full_name: Minhas, Gurdeep S last_name: Minhas citation: ama: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 2013;41(5):1265-1271. doi:10.1042/BST20130193 apa: Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., & Minhas, G. (2013). A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130193 chicago: Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford, and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” Biochemical Society Transactions. Portland Press, 2013. https://doi.org/10.1042/BST20130193. ieee: L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A long road towards the structure of respiratory complex I, a giant molecular proton pump,” Biochemical Society Transactions, vol. 41, no. 5. Portland Press, pp. 1265–1271, 2013. ista: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 41(5), 1265–1271. mla: Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” Biochemical Society Transactions, vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:10.1042/BST20130193. short: L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271. date_created: 2018-12-11T11:55:00Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:54:28Z day: '01' doi: 10.1042/BST20130193 extern: 1 intvolume: ' 41' issue: '5' month: '10' page: 1265 - 1271 publication: Biochemical Society Transactions publication_status: published publisher: Portland Press publist_id: '5106' quality_controlled: 0 status: public title: A long road towards the structure of respiratory complex I, a giant molecular proton pump type: journal_article volume: 41 year: '2013' ... --- _id: '1978' abstract: - lang: eng text: Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle. acknowledgement: This work was funded by the Medical Research Council. author: - first_name: Rozbeh full_name: 'Baradaran, Rozbeh ' last_name: Baradaran - first_name: John full_name: Berrisford, John M last_name: Berrisford - first_name: Gurdeep full_name: Minhas, Gurdeep S last_name: Minhas - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire respiratory complex i. Nature. 2013;494(7438):443-448. doi:10.1038/nature11871 apa: Baradaran, R., Berrisford, J., Minhas, G., & Sazanov, L. A. (2013). Crystal structure of the entire respiratory complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11871 chicago: Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov. “Crystal Structure of the Entire Respiratory Complex I.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature11871. ieee: R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure of the entire respiratory complex i,” Nature, vol. 494, no. 7438. Nature Publishing Group, pp. 443–448, 2013. ista: Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of the entire respiratory complex i. Nature. 494(7438), 443–448. mla: Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex I.” Nature, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48, doi:10.1038/nature11871. short: R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448. date_created: 2018-12-11T11:55:01Z date_published: 2013-02-28T00:00:00Z date_updated: 2021-01-12T06:54:28Z day: '28' doi: 10.1038/nature11871 extern: 1 intvolume: ' 494' issue: '7438' month: '02' page: 443 - 448 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5107' quality_controlled: 0 status: public title: Crystal structure of the entire respiratory complex i type: journal_article volume: 494 year: '2013' ... --- _id: '1991' abstract: - lang: eng text: Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur. acknowledgement: Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B. author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 2013;499(7458):332-335. doi:10.1038/nature12235 apa: Vicoso, B., & Bachtrog, D. (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12235 chicago: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12235. ieee: B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome in Drosophila,” Nature, vol. 499, no. 7458. Nature Publishing Group, pp. 332–335, 2013. ista: Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335. mla: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” Nature, vol. 499, no. 7458, Nature Publishing Group, 2013, pp. 332–35, doi:10.1038/nature12235. short: B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335. date_created: 2018-12-11T11:55:05Z date_published: 2013-07-18T00:00:00Z date_updated: 2021-01-12T06:54:33Z day: '18' doi: 10.1038/nature12235 extern: 1 intvolume: ' 499' issue: '7458' month: '07' page: 332 - 335 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5092' quality_controlled: 0 status: public title: Reversal of an ancient sex chromosome to an autosome in Drosophila type: journal_article volume: 499 year: '2013' ... --- _id: '1988' abstract: - lang: eng text: The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally. author: - first_name: Mike full_name: 'Bonny, Mike ' last_name: Bonny - first_name: Elisabeth full_name: Fischer-Friedrich, Elisabeth last_name: Fischer Friedrich - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse citation: ama: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003347 apa: Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., & Kruse, K. (2013). Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003347 chicago: Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille, and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003347. ieee: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation,” PLoS Computational Biology, vol. 9, no. 12. Public Library of Science, 2013. ista: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 9(12). mla: Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” PLoS Computational Biology, vol. 9, no. 12, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003347. short: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013). date_created: 2018-12-11T11:55:04Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:54:32Z day: '01' doi: 10.1371/journal.pcbi.1003347 extern: 1 intvolume: ' 9' issue: '12' month: '12' publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5095' quality_controlled: 0 status: public title: Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation type: journal_article volume: 9 year: '2013' ... --- _id: '2010' abstract: - lang: eng text: Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case. author: - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Garvesh full_name: Raskutti, Garvesh last_name: Raskutti - first_name: Peter full_name: Bühlmann, Peter last_name: Bühlmann - first_name: Bin full_name: Yu, Bin last_name: Yu citation: ama: Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 2013;41(2):436-463. doi:10.1214/12-AOS1080 apa: Uhler, C., Raskutti, G., Bühlmann, P., & Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/12-AOS1080 chicago: Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” The Annals of Statistics. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/12-AOS1080. ieee: C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” The Annals of Statistics, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013. ista: Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463. mla: Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” The Annals of Statistics, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:10.1214/12-AOS1080. short: C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463. date_created: 2018-12-11T11:55:11Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:54:42Z day: '01' department: - _id: CaUh doi: 10.1214/12-AOS1080 external_id: arxiv: - '1207.0547' intvolume: ' 41' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: www.doi.org/10.1214/12-AOS1080 month: '04' oa: 1 oa_version: Published Version page: 436 - 463 publication: The Annals of Statistics publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5066' quality_controlled: '1' scopus_import: 1 status: public title: Geometry of the faithfulness assumption in causal inference type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2013' ... --- _id: '2009' abstract: - lang: eng text: Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression. article_processing_charge: No author: - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Aleksandra full_name: Slavkovic, Aleksandra last_name: Slavkovic - first_name: Stephen full_name: Fienberg, Stephen last_name: Fienberg citation: ama: Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 2013;5(1):137-166. doi:10.29012/jpc.v5i1.629 apa: Uhler, C., Slavkovic, A., & Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . Carnegie Mellon University. https://doi.org/10.29012/jpc.v5i1.629 chicago: Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” Journal of Privacy and Confidentiality . Carnegie Mellon University, 2013. https://doi.org/10.29012/jpc.v5i1.629. ieee: C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” Journal of Privacy and Confidentiality , vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013. ista: Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166. mla: Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” Journal of Privacy and Confidentiality , vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:10.29012/jpc.v5i1.629. short: C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality 5 (2013) 137–166. date_created: 2018-12-11T11:55:11Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T06:54:41Z day: '01' department: - _id: CaUh doi: 10.29012/jpc.v5i1.629 intvolume: ' 5' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://repository.cmu.edu/jpc/vol5/iss1/6 month: '08' oa: 1 oa_version: Published Version page: 137 - 166 publication: 'Journal of Privacy and Confidentiality ' publication_status: published publisher: Carnegie Mellon University publist_id: '5067' quality_controlled: '1' status: public title: Privacy-preserving data sharing for genome-wide association studies type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2013' ... --- _id: '2074' abstract: - lang: eng text: 'Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. ' author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Vera full_name: Kaiser, Vera B last_name: Kaiser - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 2013;110(16):6453-6458. doi:10.1073/pnas.1217027110 apa: Vicoso, B., Kaiser, V., & Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1217027110 chicago: Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217027110. ieee: B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” PNAS, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013. ista: Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458. mla: Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” PNAS, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:10.1073/pnas.1217027110. short: B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458. date_created: 2018-12-11T11:55:33Z date_published: 2013-04-16T00:00:00Z date_updated: 2021-01-12T06:55:08Z day: '16' doi: 10.1073/pnas.1217027110 extern: 1 intvolume: ' 110' issue: '16' month: '04' page: 6453 - 6458 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '4964' quality_controlled: 0 status: public title: Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution type: journal_article volume: 110 year: '2013' ...