[{"year":"2014","publication":"Journal of the American Chemical Society","day":"19","page":"2711-2714","date_created":"2023-08-01T09:46:44Z","date_published":"2014-02-19T00:00:00Z","doi":"10.1021/ja411573a","publisher":"American Chemical Society","quality_controlled":"1","citation":{"apa":"Zdobinsky, T., Sankar Maiti, P., & Klajn, R. (2014). Support curvature and conformational freedom control chemical reactivity of immobilized species. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja411573a","ama":"Zdobinsky T, Sankar Maiti P, Klajn R. Support curvature and conformational freedom control chemical reactivity of immobilized species. Journal of the American Chemical Society. 2014;136(7):2711-2714. doi:10.1021/ja411573a","short":"T. Zdobinsky, P. Sankar Maiti, R. Klajn, Journal of the American Chemical Society 136 (2014) 2711–2714.","ieee":"T. Zdobinsky, P. Sankar Maiti, and R. Klajn, “Support curvature and conformational freedom control chemical reactivity of immobilized species,” Journal of the American Chemical Society, vol. 136, no. 7. American Chemical Society, pp. 2711–2714, 2014.","mla":"Zdobinsky, Tino, et al. “Support Curvature and Conformational Freedom Control Chemical Reactivity of Immobilized Species.” Journal of the American Chemical Society, vol. 136, no. 7, American Chemical Society, 2014, pp. 2711–14, doi:10.1021/ja411573a.","ista":"Zdobinsky T, Sankar Maiti P, Klajn R. 2014. Support curvature and conformational freedom control chemical reactivity of immobilized species. Journal of the American Chemical Society. 136(7), 2711–2714.","chicago":"Zdobinsky, Tino, Pradipta Sankar Maiti, and Rafal Klajn. “Support Curvature and Conformational Freedom Control Chemical Reactivity of Immobilized Species.” Journal of the American Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja411573a."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["24320557"]},"article_processing_charge":"No","author":[{"first_name":"Tino","last_name":"Zdobinsky","full_name":"Zdobinsky, Tino"},{"first_name":"Pradipta","full_name":"Sankar Maiti, Pradipta","last_name":"Sankar Maiti"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"title":"Support curvature and conformational freedom control chemical reactivity of immobilized species","publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"language":[{"iso":"eng"}],"volume":136,"issue":"7","abstract":[{"text":"We show that bimolecular reactions between species confined to the surfaces of nanoparticles can be manipulated by the nature of the linker, as well as by the curvature of the underlying particles.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 136","month":"02","date_updated":"2023-08-08T07:32:11Z","extern":"1","_id":"13403","type":"journal_article","article_type":"original","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public"},{"_id":"14018","status":"public","keyword":["Physical and Theoretical Chemistry"],"type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-22T08:58:12Z","oa_version":"None","pmid":1,"abstract":[{"text":"The sensitivities of high-harmonic generation (HHG) and strong-field ionization (SFI) to coupled electronic and nuclear dynamics are studied, using the nitric oxide (NO) molecule as an example. A coherent superposition of electronic and rotational states of NO is prepared by impulsive stimulated Raman scattering and probed by simultaneous detection of HHG and SFI yields. We observe a fourfold higher sensitivity of high-harmonic generation to electronic dynamics and attribute it to the presence of inelastic quantum paths connecting coherently related electronic states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic orders display very different sensitivities to rotational or electronic dynamics, strong-field ionization is found to be most sensitive to electronic motion. We introduce a general theoretical formalism for high-harmonic generation from coupled nuclear-electronic wave packets. We show that the unequal sensitivities of different harmonic orders to electronic or rotational dynamics result from the angle dependence of the photorecombination matrix elements which encode several autoionizing and shape resonances in the photoionization continuum of NO. We further study the dependence of rotational and electronic coherences on the intensity of the excitation pulse and support the observations with calculations.","lang":"eng"}],"month":"04","intvolume":" 171","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"publication_status":"published","volume":171,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Baykusheva, Denitsa Rangelova, Peter M. Kraus, Song Bin Zhang, Nina Rohringer, and Hans Jakob Wörner. “The Sensitivities of High-Harmonic Generation and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4fd00018h.","ista":"Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. 2014. The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. 171, 113–132.","mla":"Baykusheva, Denitsa Rangelova, et al. “The Sensitivities of High-Harmonic Generation and Strong-Field Ionization to Coupled Electronic and Nuclear Dynamics.” Faraday Discussions, vol. 171, Royal Society of Chemistry, 2014, pp. 113–32, doi:10.1039/c4fd00018h.","short":"D.R. Baykusheva, P.M. Kraus, S.B. Zhang, N. Rohringer, H.J. Wörner, Faraday Discussions 171 (2014) 113–132.","ieee":"D. R. Baykusheva, P. M. Kraus, S. B. Zhang, N. Rohringer, and H. J. Wörner, “The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics,” Faraday Discussions, vol. 171. Royal Society of Chemistry, pp. 113–132, 2014.","ama":"Baykusheva DR, Kraus PM, Zhang SB, Rohringer N, Wörner HJ. The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. 2014;171:113-132. doi:10.1039/c4fd00018h","apa":"Baykusheva, D. R., Kraus, P. M., Zhang, S. B., Rohringer, N., & Wörner, H. J. (2014). The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00018h"},"title":"The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics","author":[{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"last_name":"Kraus","full_name":"Kraus, Peter M.","first_name":"Peter M."},{"first_name":"Song Bin","last_name":"Zhang","full_name":"Zhang, Song Bin"},{"first_name":"Nina","last_name":"Rohringer","full_name":"Rohringer, Nina"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"article_processing_charge":"No","external_id":{"pmid":["25415558"]},"publisher":"Royal Society of Chemistry","quality_controlled":"1","day":"14","publication":"Faraday Discussions","year":"2014","date_published":"2014-04-14T00:00:00Z","doi":"10.1039/c4fd00018h","date_created":"2023-08-10T06:38:19Z","page":"113-132"},{"issue":"6","volume":141,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","month":"08","intvolume":" 141","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.","lang":"eng"}],"extern":"1","date_updated":"2023-08-22T09:01:31Z","status":"public","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"type":"journal_article","article_type":"original","_id":"14019","doi":"10.1063/1.4890744","date_published":"2014-08-14T00:00:00Z","date_created":"2023-08-10T06:38:30Z","day":"14","publication":"The Journal of Chemical Physics","year":"2014","quality_controlled":"1","publisher":"AIP Publishing","title":"The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra","author":[{"first_name":"K.","full_name":"Vasilatou, K.","last_name":"Vasilatou"},{"first_name":"J. M.","full_name":"Michaud, J. M.","last_name":"Michaud"},{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Grassi","full_name":"Grassi, G.","first_name":"G."},{"last_name":"Merkt","full_name":"Merkt, F.","first_name":"F."}],"external_id":{"pmid":["25134581"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal of Chemical Physics 141 (2014).","ieee":"K. Vasilatou, J. M. Michaud, D. R. Baykusheva, G. Grassi, and F. Merkt, “The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra,” The Journal of Chemical Physics, vol. 141, no. 6. AIP Publishing, 2014.","ama":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. 2014;141(6). doi:10.1063/1.4890744","apa":"Vasilatou, K., Michaud, J. M., Baykusheva, D. R., Grassi, G., & Merkt, F. (2014). The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4890744","mla":"Vasilatou, K., et al. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of Chemical Physics, vol. 141, no. 6, 064317, AIP Publishing, 2014, doi:10.1063/1.4890744.","ista":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. 2014. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. 141(6), 064317.","chicago":"Vasilatou, K., J. M. Michaud, Denitsa Rangelova Baykusheva, G. Grassi, and F. Merkt. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” The Journal of Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4890744."},"article_number":"064317"},{"date_created":"2023-08-10T06:38:48Z","date_published":"2014-06-10T00:00:00Z","doi":"10.1088/0953-4075/47/12/124030","publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","day":"10","year":"2014","oa":1,"quality_controlled":"1","publisher":"IOP Publishing","title":"Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules","article_processing_charge":"No","external_id":{"arxiv":["1311.3923"]},"author":[{"full_name":"Kraus, P M","last_name":"Kraus","first_name":"P M"},{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"first_name":"H J","last_name":"Wörner","full_name":"Wörner, H J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 47(12), 124030.","chicago":"Kraus, P M, Denitsa Rangelova Baykusheva, and H J Wörner. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2014. https://doi.org/10.1088/0953-4075/47/12/124030.","ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 2014;47(12). doi:10.1088/0953-4075/47/12/124030","apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/0953-4075/47/12/124030","short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 47 (2014).","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12. IOP Publishing, 2014.","mla":"Kraus, P. M., et al. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12, 124030, IOP Publishing, 2014, doi:10.1088/0953-4075/47/12/124030."},"article_number":"124030","issue":"12","volume":47,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0953-4075"],"eissn":["1361-6455"]},"intvolume":" 47","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1311.3923","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We present the detailed analysis of a new two-pulse orientation scheme that achieves macroscopic field-free orientation at the high particle densities required for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923). Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour non-resonant femtosecond laser pulses. High-harmonic generation is used to probe the oriented wave-packet dynamics and reveals that a very high degree of orientation (Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting carbonyl sulphide molecules. We show that the present two-pulse scheme selectively enhances orientation created by the hyperpolarizability interaction whereas the ionization-depletion mechanism plays no role. We further control and optimize orientation through the delay between the one- and two-colour pump pulses. Finally, we demonstrate a complementary encoding of electronic-structure features, such as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress makes two-pulse field-free orientation an attractive tool for a broad class of time-resolved measurements.","lang":"eng"}],"extern":"1","date_updated":"2023-08-22T09:04:30Z","keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"status":"public","article_type":"original","type":"journal_article","_id":"14021"},{"extern":"1","date_updated":"2023-08-22T09:02:56Z","_id":"14020","status":"public","keyword":["General Physics and Astronomy"],"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","volume":113,"issue":"2","pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We report the observation of macroscopic field-free orientation, i.e., more than 73% of CO molecules pointing in the same direction. This is achieved through an all-optical scheme operating at high particle densities (>10(17) cm(-3)) that combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses. We show that the achieved orientation solely relies on the hyperpolarizability interaction as opposed to an ionization-depletion mechanism, thus, opening a wide range of applications. The achieved strong orientation enables us to reveal the molecular-frame anisotropies of the photorecombination amplitudes and phases caused by a shape resonance. The resonance appears as a local maximum in the even-harmonic emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in this spectral region through the combined effects of an asymmetric photorecombination phase and a subcycle Stark effect, generic for polar molecules, that we experimentally identify."}],"month":"07","intvolume":" 113","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1311.3923","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 113(2), 023001.","chicago":"Kraus, P. M., Denitsa Rangelova Baykusheva, and H. J. Wörner. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.113.023001.","short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Physical Review Letters 113 (2014).","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse field-free orientation reveals anisotropy of molecular shape resonance,” Physical Review Letters, vol. 113, no. 2. American Physical Society, 2014.","ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 2014;113(2). doi:10.1103/physrevlett.113.023001","apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.113.023001","mla":"Kraus, P. M., et al. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters, vol. 113, no. 2, 023001, American Physical Society, 2014, doi:10.1103/physrevlett.113.023001."},"title":"Two-pulse field-free orientation reveals anisotropy of molecular shape resonance","author":[{"full_name":"Kraus, P. M.","last_name":"Kraus","first_name":"P. M."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Wörner","full_name":"Wörner, H. J.","first_name":"H. J."}],"external_id":{"pmid":["25062172"],"arxiv":["1311.3923"]},"article_processing_charge":"No","article_number":"023001","day":"11","publication":"Physical Review Letters","year":"2014","date_published":"2014-07-11T00:00:00Z","doi":"10.1103/physrevlett.113.023001","date_created":"2023-08-10T06:38:38Z","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"page":"457 - 492","date_created":"2018-12-11T11:47:01Z","doi":"10.1007/s00453-013-9843-7","date_published":"2014-11-01T00:00:00Z","year":"2014","publication":"Algorithmica","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer","article_processing_charge":"No","external_id":{"arxiv":["1604.08234"]},"publist_id":"7282","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"title":"Polynomial-time algorithms for energy games with special weight structures","citation":{"mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:10.1007/s00453-013-9843-7.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 2014;70(3):457-492. doi:10.1007/s00453-013-9843-7","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. Algorithmica. Springer. https://doi.org/10.1007/s00453-013-9843-7","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” Algorithmica, vol. 70, no. 3. Springer, pp. 457–492, 2014.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7.","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10905"}]},"volume":70,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1604.08234","open_access":"1"}],"scopus_import":"1","intvolume":" 70","month":"11","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help."}],"oa_version":"Preprint","department":[{"_id":"KrCh"}],"date_updated":"2023-09-05T14:09:29Z","type":"journal_article","article_type":"original","status":"public","_id":"535"},{"title":"Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature","department":[{"_id":"HeEd"}],"article_processing_charge":"No","author":[{"first_name":"Valentin","last_name":"Zobel","full_name":"Zobel, Valentin"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan","last_name":"Reininghaus"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In Topological Methods in Data Analysis and Visualization III (pp. 249–262). Springer. https://doi.org/10.1007/978-3-319-04099-8_16","ama":"Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In: Topological Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–262.","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature,” in Topological Methods in Data Analysis and Visualization III , 2014, pp. 249–262.","mla":"Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.","ista":"Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. Topological Methods in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In Topological Methods in Data Analysis and Visualization III , 249–62. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_16."},"date_updated":"2023-09-05T14:13:16Z","status":"public","type":"conference","_id":"10886","date_created":"2022-03-18T13:05:39Z","date_published":"2014-03-19T00:00:00Z","doi":"10.1007/978-3-319-04099-8_16","page":"249-262","language":[{"iso":"eng"}],"publication":"Topological Methods in Data Analysis and Visualization III ","day":"19","publication_status":"published","year":"2014","publication_identifier":{"eisbn":["9783319040998"],"issn":["1612-3786"],"isbn":["9783319040981"],"eissn":["2197-666X"]},"month":"03","publisher":"Springer","alternative_title":["Mathematics and Visualization"],"quality_controlled":"1","scopus_import":"1","acknowledgement":"This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.","oa_version":"None","abstract":[{"lang":"eng","text":"We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set."}]},{"department":[{"_id":"CaHe"}],"date_updated":"2023-09-05T14:12:00Z","status":"public","type":"book_chapter","_id":"6178","series_title":"Methods in Molecular Biology","volume":1189,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781493911639","9781493911646"]},"publication_status":"published","place":"New York, NY","month":"08","intvolume":" 1189","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo."}],"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","editor":[{"full_name":"Nelson, Celeste","last_name":"Nelson","first_name":"Celeste"}],"author":[{"orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"full_name":"Campinho, Pedro","orcid":"0000-0002-8526-5416","last_name":"Campinho","first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["25245697"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In Tissue Morphogenesis, edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York, NY: Springer, 2014. https://doi.org/10.1007/978-1-4939-1164-6_15.","ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. Tissue Morphogenesis. Vol 1189. Methods in Molecular Biology. New York, NY: Springer; 2014:219-235. doi:10.1007/978-1-4939-1164-6_15","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., & Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), Tissue Morphogenesis (Vol. 1189, pp. 219–235). New York, NY: Springer. https://doi.org/10.1007/978-1-4939-1164-6_15","ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in Tissue Morphogenesis, vol. 1189, C. Nelson, Ed. New York, NY: Springer, 2014, pp. 219–235.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” Tissue Morphogenesis, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:10.1007/978-1-4939-1164-6_15."},"date_published":"2014-08-22T00:00:00Z","doi":"10.1007/978-1-4939-1164-6_15","date_created":"2019-03-26T08:55:59Z","page":"219-235","day":"22","publication":"Tissue Morphogenesis","year":"2014","publisher":"Springer","quality_controlled":"1"},{"day":"01","publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-0456"],"eissn":["1869-7135"]},"year":"2014","publication_status":"published","volume":116,"date_published":"2014-03-01T00:00:00Z","doi":"10.1365/s13291-014-0083-9","date_created":"2022-03-04T07:54:39Z","page":"21-41","oa_version":"None","abstract":[{"lang":"eng","text":"We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field."}],"month":"03","intvolume":" 116","quality_controlled":"1","publisher":"Springer Nature","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","chicago":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature, 2014. https://doi.org/10.1365/s13291-014-0083-9.","ama":"Seiringer R. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 2014;116:21-41. doi:10.1365/s13291-014-0083-9","apa":"Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions. Jahresbericht Der Deutschen Mathematiker-Vereinigung. Springer Nature. https://doi.org/10.1365/s13291-014-0083-9","short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41.","ieee":"R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,” Jahresbericht der Deutschen Mathematiker-Vereinigung, vol. 116. Springer Nature, pp. 21–41, 2014.","mla":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” Jahresbericht Der Deutschen Mathematiker-Vereinigung, vol. 116, Springer Nature, 2014, pp. 21–41, doi:10.1365/s13291-014-0083-9."},"date_updated":"2023-09-05T14:19:47Z","department":[{"_id":"RoSe"}],"title":"The excitation spectrum for Bose fluids with weak interactions","author":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"article_processing_charge":"No","_id":"10814","status":"public","keyword":["General Medicine"],"type":"journal_article","article_type":"original"},{"type":"book_chapter","status":"public","series_title":"Mathematics and Visualization","_id":"10817","department":[{"_id":"HeEd"}],"date_updated":"2023-09-05T15:33:45Z","scopus_import":"1","place":"Cham","month":"03","abstract":[{"lang":"eng","text":"The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption."}],"oa_version":"None","ec_funded":1,"publication_status":"published","publication_identifier":{"issn":["1612-3786"],"isbn":["9783319040981"],"eissn":["2197-666X"],"eisbn":["9783319040998"]},"language":[{"iso":"eng"}],"project":[{"name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_processing_charge":"No","author":[{"last_name":"Günther","full_name":"Günther, David","first_name":"David"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Reininghaus, Jan","last_name":"Reininghaus"},{"first_name":"Hans-Peter","last_name":"Seidel","full_name":"Seidel, Hans-Peter"},{"last_name":"Weinkauf","full_name":"Weinkauf, Tino","first_name":"Tino"}],"title":"Notes on the simplification of the Morse-Smale complex","editor":[{"first_name":"Peer-Timo","full_name":"Bremer, Peer-Timo","last_name":"Bremer"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"},{"full_name":"Pascucci, Valerio","last_name":"Pascucci","first_name":"Valerio"},{"first_name":"Ronald","last_name":"Peikert","full_name":"Peikert, Ronald"}],"citation":{"apa":"Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9","ama":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9","short":"D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III., Springer Nature, Cham, 2014, pp. 135–150.","ieee":"D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the simplification of the Morse-Smale complex,” in Topological Methods in Data Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.","mla":"Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.” Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.","ista":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization III. , 135–150.","chicago":"Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf. “Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.","page":"135-150","date_created":"2022-03-04T08:33:57Z","date_published":"2014-03-19T00:00:00Z","doi":"10.1007/978-3-319-04099-8_9","year":"2014","publication":"Topological Methods in Data Analysis and Visualization III.","day":"19"},{"citation":{"chicago":"Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and Technology Austria, 2014.","ista":"Konrad M. 2014. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","mla":"Konrad, Matthias. Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus. Institute of Science and Technology Austria, 2014.","ieee":"M. Konrad, “Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology Austria, 2014.","short":"M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology Austria, 2014.","apa":"Konrad, M. (2014). Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","ama":"Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 2014."},"date_updated":"2023-09-07T11:38:56Z","supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","last_name":"Cremer","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","publist_id":"5814","author":[{"first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","full_name":"Konrad, Matthias"}],"department":[{"_id":"SyCr"}],"title":"Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus","_id":"1395","type":"dissertation","status":"public","degree_awarded":"PhD","year":"2014","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"day":"01","page":"131","date_created":"2018-12-11T11:51:46Z","date_published":"2014-02-01T00:00:00Z","abstract":[{"text":"In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants.","lang":"eng"}],"oa_version":"None","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"month":"02"},{"oa_version":"None","abstract":[{"text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.","lang":"eng"}],"month":"12","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"year":"2014","degree_awarded":"PhD","publication_status":"published","date_published":"2014-12-01T00:00:00Z","date_created":"2018-12-11T11:51:49Z","page":"90","_id":"1402","status":"public","type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"citation":{"ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.","ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014.","apa":"Marhavá, P. (2014). Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","mla":"Marhavá, Petra. Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2014."},"date_updated":"2023-09-07T11:39:38Z","department":[{"_id":"JiFr"}],"title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","publist_id":"5805","author":[{"last_name":"Marhavá","full_name":"Marhavá, Petra","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 50(1), 164–177.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” Journal of Mathematical Imaging and Vision. Springer, 2014. https://doi.org/10.1007/s10851-013-0468-x.","ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 2014;50(1):164-177. doi:10.1007/s10851-013-0468-x","apa":"Edelsbrunner, H., & Pausinger, F. (2014). Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. Springer. https://doi.org/10.1007/s10851-013-0468-x","short":"H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision 50 (2014) 164–177.","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” Journal of Mathematical Imaging and Vision, vol. 50, no. 1. Springer, pp. 164–177, 2014.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” Journal of Mathematical Imaging and Vision, vol. 50, no. 1, Springer, 2014, pp. 164–77, doi:10.1007/s10851-013-0468-x."},"title":"Stable length estimates of tube-like shapes","author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian"}],"publist_id":"4691","publisher":"Springer","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Mathematical Imaging and Vision","has_accepted_license":"1","year":"2014","doi":"10.1007/s10851-013-0468-x","date_published":"2014-09-01T00:00:00Z","date_created":"2018-12-11T11:56:36Z","page":"164 - 177","_id":"2255","status":"public","pubrep_id":"549","type":"journal_article","ddc":["000"],"date_updated":"2023-09-07T11:41:25Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:35Z","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm."}],"month":"09","intvolume":" 50","scopus_import":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"2f93f3e63a38a85cd4404d7953913b14","file_id":"5204","date_updated":"2020-07-14T12:45:35Z","file_size":3941391,"creator":"system","date_created":"2018-12-12T10:16:18Z","file_name":"IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09249907"]},"publication_status":"published","volume":50,"issue":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2843"},{"relation":"dissertation_contains","status":"public","id":"1399"}]},"ec_funded":1},{"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4735","checksum":"2aae223fee8ffeaf57bbabd8d92b6a2c","file_size":914396,"date_updated":"2020-07-14T12:45:30Z","creator":"system","file_name":"IST-2016-534-v1+1_Eliminating_Tverberg_points_I._An_analogue_of_the_Whitney_trick.pdf","date_created":"2018-12-12T10:09:12Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1123"}]},"abstract":[{"text":"Motivated by topological Tverberg-type problems, we consider multiple (double, triple, and higher multiplicity) selfintersection points of maps from finite simplicial complexes (compact polyhedra) into ℝd and study conditions under which such multiple points can be eliminated. The most classical case is that of embeddings (i.e., maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem, the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary condition for embeddability (namely, vanishing of the van Kampen ob-struction). For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes then one can successively remove these double points by local modifications of the map f. One of the main tools is the famous Whitney trick that permits eliminating pairs of double points of opposite intersection sign. We are interested in generalizing this approach to intersection points of higher multiplicity. We call a point y 2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e., does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time algorithm for deciding this (based on the vanishing of a cohomological obstruction, as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney trick: Given r pairwise disjoint simplices of K such that the intersection of their images contains two r-fold Tverberg points y+ and y- of opposite intersection sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper, we plan to develop this further and present a generalization of the classical Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability of κ-complexes into ℝd for a wider range of dimensions) to intersection points of higher multiplicity.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"06","date_updated":"2023-09-07T11:56:27Z","ddc":["510"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:30Z","_id":"2159","type":"conference","conference":{"location":"Kyoto, Japan","end_date":"2014-06-11","start_date":"2014-06-08","name":"SoCG: Symposium on Computational Geometry"},"status":"public","pubrep_id":"534","has_accepted_license":"1","year":"2014","day":"08","publication":"Proceedings of the Annual Symposium on Computational Geometry","page":"171 - 180","doi":"10.1145/2582112.2582134","date_published":"2014-06-08T00:00:00Z","date_created":"2018-12-11T11:56:03Z","acknowledgement":"Swiss National Science Foundation (Project SNSF-PP00P2-138948)","quality_controlled":"1","publisher":"ACM","oa":1,"citation":{"mla":"Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue of the Whitney Trick.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 171–80, doi:10.1145/2582112.2582134.","apa":"Mabillard, I., & Wagner, U. (2014). Eliminating Tverberg points, I. An analogue of the Whitney trick. In Proceedings of the Annual Symposium on Computational Geometry (pp. 171–180). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582134","ama":"Mabillard I, Wagner U. Eliminating Tverberg points, I. An analogue of the Whitney trick. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:171-180. doi:10.1145/2582112.2582134","short":"I. Mabillard, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 171–180.","ieee":"I. Mabillard and U. Wagner, “Eliminating Tverberg points, I. An analogue of the Whitney trick,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 171–180.","chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Tverberg Points, I. An Analogue of the Whitney Trick.” In Proceedings of the Annual Symposium on Computational Geometry, 171–80. ACM, 2014. https://doi.org/10.1145/2582112.2582134.","ista":"Mabillard I, Wagner U. 2014. Eliminating Tverberg points, I. An analogue of the Whitney trick. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 171–180."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Mabillard","full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"publist_id":"4847","title":"Eliminating Tverberg points, I. An analogue of the Whitney trick"},{"file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"NiBa"}],"date_updated":"2023-09-07T11:55:53Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"462","_id":"2023","related_material":{"record":[{"id":"1125","status":"public","relation":"dissertation_contains"}]},"issue":"24","volume":4,"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4946","checksum":"9ab43db1b0fede7bfe560ed77e177b76","creator":"system","file_size":118813,"date_updated":"2020-07-14T12:45:25Z","file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:12:28Z"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"11","intvolume":" 4","abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"oa_version":"Published Version","publist_id":"5049","author":[{"last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","citation":{"mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1289","ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597. doi:10.1002/ece3.1289","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” Ecology and Evolution, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"page":"4589 - 4597","doi":"10.1002/ece3.1289","date_published":"2014-11-27T00:00:00Z","date_created":"2018-12-11T11:55:16Z","has_accepted_license":"1","year":"2014","day":"27","publication":"Ecology and Evolution","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1},{"abstract":[{"lang":"eng","text":"While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs."}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38"}],"month":"07","intvolume":" 8559","publication_identifier":{"isbn":["978-331908866-2"]},"publication_status":"published","file":[{"date_created":"2018-12-12T10:13:14Z","file_name":"IST-2014-297-v1+1_cav14-final.pdf","date_updated":"2020-07-14T12:45:33Z","file_size":416732,"creator":"system","file_id":"4995","checksum":"a631d3105509f239724644e77a1212e2","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f8b0f748cc9fa697ca992cc56c87bc4e","file_id":"4996","date_updated":"2020-07-14T12:45:33Z","file_size":616293,"creator":"system","date_created":"2018-12-12T10:13:15Z","file_name":"IST-2014-297-v2+1_cav14-final2.pdf"}],"language":[{"iso":"eng"}],"volume":8559,"related_material":{"record":[{"status":"public","id":"1130","relation":"dissertation_contains"}]},"ec_funded":1,"_id":"2218","type":"conference","conference":{"name":"CAV: Computer Aided Verification","start_date":"2014-07-18","end_date":"2014-07-22","location":"Vienna, Austria"},"status":"public","pubrep_id":"297","date_updated":"2023-09-07T11:57:01Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:33Z","department":[{"_id":"ToHe"}],"publisher":"Springer","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2014","day":"22","page":"568 - 584","doi":"10.1007/978-3-319-08867-9_38","date_published":"2014-07-22T00:00:00Z","date_created":"2018-12-11T11:56:23Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Cerny, Pavol, et al. Regression-Free Synthesis for Concurrency. Vol. 8559, Springer, 2014, pp. 568–84, doi:10.1007/978-3-319-08867-9_38.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2014, pp. 568–584.","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free synthesis for concurrency,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 568–584.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach, T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_38","ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:10.1007/978-3-319-08867-9_38","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_38.","ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559, 568–584."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Pavol","full_name":"Cerny, Pavol","last_name":"Cerny"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten","last_name":"Tarrach"}],"publist_id":"4749","title":"Regression-free synthesis for concurrency"},{"month":"03","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1904.07083","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing. In this paper, we study compositional properties of the ioco-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the ioco conformance relation, the resulting methodology can be applied to a broader class of systems."}],"related_material":{"record":[{"relation":"earlier_version","id":"5411","status":"public"},{"relation":"dissertation_contains","id":"1155","status":"public"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2159-4848"],"isbn":["978-1-4799-2255-0"]},"publication_status":"published","status":"public","type":"conference","conference":{"location":"Cleveland, USA","end_date":"2014-04-04","start_date":"2014-03-31","name":"ICST: International Conference on Software Testing, Verification and Validation"},"_id":"2167","department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T11:58:33Z","quality_controlled":"1","publisher":"IEEE","oa":1,"date_published":"2014-03-01T00:00:00Z","doi":"10.1109/ICST.2014.50","date_created":"2018-12-11T11:56:06Z","day":"01","publication":"IEEE 7th International Conference on Software Testing, Verification and Validation","year":"2014","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"article_number":"6823899","title":"Compositional specifications for IOCO testing","author":[{"last_name":"Daca","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Willibald","last_name":"Krenn","full_name":"Krenn, Willibald"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"}],"publist_id":"4817","article_processing_charge":"No","external_id":{"arxiv":["1904.07083"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing. IEEE 7th International Conference on Software Testing, Verification and Validation. ICST: International Conference on Software Testing, Verification and Validation, 6823899.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. “Compositional Specifications for IOCO Testing.” In IEEE 7th International Conference on Software Testing, Verification and Validation. IEEE, 2014. https://doi.org/10.1109/ICST.2014.50.","ieee":"P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, “Compositional specifications for IOCO testing,” in IEEE 7th International Conference on Software Testing, Verification and Validation, Cleveland, USA, 2014.","short":"P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, in:, IEEE 7th International Conference on Software Testing, Verification and Validation, IEEE, 2014.","ama":"Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional specifications for IOCO testing. In: IEEE 7th International Conference on Software Testing, Verification and Validation. IEEE; 2014. doi:10.1109/ICST.2014.50","apa":"Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional specifications for IOCO testing. In IEEE 7th International Conference on Software Testing, Verification and Validation. Cleveland, USA: IEEE. https://doi.org/10.1109/ICST.2014.50","mla":"Daca, Przemyslaw, et al. “Compositional Specifications for IOCO Testing.” IEEE 7th International Conference on Software Testing, Verification and Validation, 6823899, IEEE, 2014, doi:10.1109/ICST.2014.50."}},{"date_updated":"2023-09-07T11:58:33Z","citation":{"mla":"Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. Vol. 8559, Springer, 2014, pp. 473–90, doi:10.1007/978-3-319-08867-9_31.","short":"K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 473–490.","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2014). CEGAR for qualitative analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_31","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic systems. In: Vol 8559. Springer; 2014:473-490. doi:10.1007/978-3-319-08867-9_31","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_31.","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4978","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"last_name":"Daca","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"CEGAR for qualitative analysis of probabilistic systems","_id":"2063","type":"conference","conference":{"location":"Vienna, Austria","end_date":"2014-07-22","start_date":"2014-07-18","name":"CAV: Computer Aided Verification"},"status":"public","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"year":"2014","publication_status":"published","day":"01","language":[{"iso":"eng"}],"page":"473 - 490","date_published":"2014-07-01T00:00:00Z","doi":"10.1007/978-3-319-08867-9_31","related_material":{"record":[{"status":"public","id":"5412","relation":"earlier_version"},{"id":"5413","status":"public","relation":"earlier_version"},{"id":"5414","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","id":"1155","status":"public"}]},"volume":8559,"date_created":"2018-12-11T11:55:30Z","ec_funded":1,"abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements.","lang":"eng"}],"oa_version":"None","publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":"1","month":"07","intvolume":" 8559"},{"department":[{"_id":"ToBo"}],"date_updated":"2023-09-07T12:00:25Z","type":"journal_article","status":"public","_id":"2001","issue":"6","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"818"}]},"volume":6,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"month":"06","intvolume":" 6","abstract":[{"lang":"eng","text":"Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria."}],"oa_version":"None","publist_id":"5076","author":[{"last_name":"Mitosch","full_name":"Mitosch, Karin","first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"}],"title":"Bacterial responses to antibiotics and their combinations","citation":{"chicago":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” Environmental Microbiology Reports. Wiley, 2014. https://doi.org/10.1111/1758-2229.12190.","ista":"Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 6(6), 545–557.","mla":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” Environmental Microbiology Reports, vol. 6, no. 6, Wiley, 2014, pp. 545–57, doi:10.1111/1758-2229.12190.","apa":"Mitosch, K., & Bollenbach, M. T. (2014). Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.12190","ama":"Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 2014;6(6):545-557. doi:10.1111/1758-2229.12190","ieee":"K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their combinations,” Environmental Microbiology Reports, vol. 6, no. 6. Wiley, pp. 545–557, 2014.","short":"K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014) 545–557."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"page":"545 - 557","doi":"10.1111/1758-2229.12190","date_published":"2014-06-22T00:00:00Z","date_created":"2018-12-11T11:55:08Z","year":"2014","day":"22","publication":"Environmental Microbiology Reports","publisher":"Wiley","quality_controlled":"1"},{"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Gazi, K.Z. Pietrzak, M. Rybar, in:, J. Garay, R. Gennaro (Eds.), Springer, 2014, pp. 113–130.","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact PRF-security of NMAC and HMAC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA, 2014, vol. 8616, no. 1, pp. 113–130.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact PRF-security of NMAC and HMAC. In: Garay J, Gennaro R, eds. Vol 8616. Springer; 2014:113-130. doi:10.1007/978-3-662-44371-2_7","apa":"Gazi, P., Pietrzak, K. Z., & Rybar, M. (2014). The exact PRF-security of NMAC and HMAC. In J. Garay & R. Gennaro (Eds.) (Vol. 8616, pp. 113–130). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, USA: Springer. https://doi.org/10.1007/978-3-662-44371-2_7","mla":"Gazi, Peter, et al. The Exact PRF-Security of NMAC and HMAC. Edited by Juan Garay and Rosario Gennaro, vol. 8616, no. 1, Springer, 2014, pp. 113–30, doi:10.1007/978-3-662-44371-2_7.","ista":"Gazi P, Pietrzak KZ, Rybar M. 2014. The exact PRF-security of NMAC and HMAC. CRYPTO: International Cryptology Conference, LNCS, vol. 8616, 113–130.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact PRF-Security of NMAC and HMAC.” edited by Juan Garay and Rosario Gennaro, 8616:113–30. Springer, 2014. https://doi.org/10.1007/978-3-662-44371-2_7."},"editor":[{"last_name":"Garay","full_name":"Garay, Juan","first_name":"Juan"},{"full_name":"Gennaro, Rosario","last_name":"Gennaro","first_name":"Rosario"}],"title":"The exact PRF-security of NMAC and HMAC","author":[{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar","full_name":"Rybar, Michal"}],"publist_id":"4955","oa":1,"publisher":"Springer","quality_controlled":"1","day":"01","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:55:36Z","doi":"10.1007/978-3-662-44371-2_7","date_published":"2014-01-01T00:00:00Z","page":"113 - 130","_id":"2082","pubrep_id":"682","status":"public","conference":{"name":"CRYPTO: International Cryptology Conference","end_date":"2014-08-21","location":"Santa Barbara, USA","start_date":"2014-08-17"},"type":"conference","ddc":["000","004"],"date_updated":"2023-09-07T12:02:27Z","file_date_updated":"2020-07-14T12:45:28Z","department":[{"_id":"KrPi"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC was introduced by Bellare, Canetti and Krawczyk [Crypto'96], who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1) f is a PRF and (2) the function we get when cascading f is weakly collision-resistant. Unfortunately, HMAC is typically instantiated with cryptographic hash functions like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable guarantees for NMAC, Bellare [Crypto'06] showed its security based solely on the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first contribution is a simpler and uniform proof for this fact: If f is an ε-secure PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries), then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security of a modification of NMAC called NI [An and Bellare, Crypto'99] that differs mainly by using a compression function with an additional keying input. This avoids the constant rekeying on multi-block messages in NMAC and allows for a security proof starting by the standard switch from a PRF to a random function, followed by an information-theoretic analysis. We carry out such an analysis, obtaining a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c. The proof borrows combinatorial techniques originally developed for proving the security of CBC-MAC [Bellare et al., Crypto'05]."}],"intvolume":" 8616","month":"01","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"file":[{"checksum":"dab6ab36a5f6af94f2b597e6404ed11d","file_id":"4999","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-682-v1+1_578.pdf","date_created":"2018-12-12T10:13:17Z","creator":"system","file_size":492310,"date_updated":"2020-07-14T12:45:28Z"}],"publication_status":"published","ec_funded":1,"volume":8616,"issue":"1","related_material":{"record":[{"id":"838","status":"public","relation":"dissertation_contains"}]}},{"publication_status":"published","language":[{"iso":"eng"}],"volume":31,"related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"}]},"issue":"6","abstract":[{"text":"Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/25535919"}],"scopus_import":"1","intvolume":" 31","month":"12","date_updated":"2023-09-07T12:05:08Z","department":[{"_id":"CaHe"}],"_id":"1912","type":"journal_article","status":"public","year":"2014","publication":"Developmental Cell","day":"22","page":"774 - 783","date_created":"2018-12-11T11:54:41Z","date_published":"2014-12-22T00:00:00Z","doi":"10.1016/j.devcel.2014.11.003","acknowledgement":"We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus, and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing reagents. This work was supported by the Institute of Science and Technology Austria and an Alexander von Humboldt Foundation fellowship to J.C.","oa":1,"quality_controlled":"1","publisher":"Cell Press","citation":{"mla":"Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell, vol. 31, no. 6, Cell Press, 2014, pp. 774–83, doi:10.1016/j.devcel.2014.11.003.","ieee":"J. Compagnon et al., “The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ,” Developmental Cell, vol. 31, no. 6. Cell Press, pp. 774–783, 2014.","short":"J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha, M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.","apa":"Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K., Behrndt, M., & Heisenberg, C.-P. J. (2014). The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2014.11.003","ama":"Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 2014;31(6):774-783. doi:10.1016/j.devcel.2014.11.003","chicago":"Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier, Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell. Cell Press, 2014. https://doi.org/10.1016/j.devcel.2014.11.003.","ista":"Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["25535919"]},"publist_id":"5182","author":[{"last_name":"Compagnon","full_name":"Compagnon, Julien","first_name":"Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone"},{"last_name":"Rajshekar","full_name":"Rajshekar, Srivarsha","first_name":"Srivarsha"},{"first_name":"Rita","full_name":"Kottmeier, Rita","last_name":"Kottmeier"},{"last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"title":"The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ"},{"citation":{"apa":"Grusch, M., Schelch, K., Riedler, R., Gschaider-Reichhart, E., Differ, C., Berger, W., … Janovjak, H. L. (2014). Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. Wiley-Blackwell. https://doi.org/10.15252/embj.201387695","ama":"Grusch M, Schelch K, Riedler R, et al. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 2014;33(15):1713-1726. doi:10.15252/embj.201387695","short":"M. Grusch, K. Schelch, R. Riedler, E. Gschaider-Reichhart, C. Differ, W. Berger, Á. Inglés Prieto, H.L. Janovjak, EMBO Journal 33 (2014) 1713–1726.","ieee":"M. Grusch et al., “Spatio-temporally precise activation of engineered receptor tyrosine kinases by light,” EMBO Journal, vol. 33, no. 15. Wiley-Blackwell, pp. 1713–1726, 2014.","mla":"Grusch, Michael, et al. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal, vol. 33, no. 15, Wiley-Blackwell, 2014, pp. 1713–26, doi:10.15252/embj.201387695.","ista":"Grusch M, Schelch K, Riedler R, Gschaider-Reichhart E, Differ C, Berger W, Inglés Prieto Á, Janovjak HL. 2014. Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO Journal. 33(15), 1713–1726.","chicago":"Grusch, Michael, Karin Schelch, Robert Riedler, Eva Gschaider-Reichhart, Christopher Differ, Walter Berger, Álvaro Inglés Prieto, and Harald L Janovjak. “Spatio-Temporally Precise Activation of Engineered Receptor Tyrosine Kinases by Light.” EMBO Journal. Wiley-Blackwell, 2014. https://doi.org/10.15252/embj.201387695."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Grusch, Michael","last_name":"Grusch","first_name":"Michael"},{"full_name":"Schelch, Karin","last_name":"Schelch","first_name":"Karin"},{"first_name":"Robert","last_name":"Riedler","full_name":"Riedler, Robert"},{"first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart"},{"first_name":"Christopher","last_name":"Differ","full_name":"Differ, Christopher"},{"last_name":"Berger","full_name":"Berger, Walter","first_name":"Walter"},{"last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4953","title":"Spatio-temporally precise activation of engineered receptor tyrosine kinases by light","acknowledgement":"European Union Seventh Framework Programme; Human Frontier Science Program; Oesterreichische Nationalbank Anniversary Fund 14211; Austrian Research Promotion Agency; FemTech","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"year":"2014","day":"01","publication":"EMBO Journal","page":"1713 - 1726","doi":"10.15252/embj.201387695","date_published":"2014-07-01T00:00:00Z","date_created":"2018-12-11T11:55:37Z","_id":"2084","type":"journal_article","status":"public","date_updated":"2023-09-07T12:49:09Z","department":[{"_id":"HaJa"}],"abstract":[{"lang":"eng","text":"Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194103/"}],"month":"07","intvolume":" 33","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"418","status":"public","relation":"dissertation_contains"}]},"issue":"15","volume":33},{"page":"78 - 84","date_created":"2018-12-11T11:56:02Z","doi":"10.1145/2582112.2582137","related_material":{"record":[{"relation":"later_version","status":"public","id":"425"}]},"date_published":"2014-06-01T00:00:00Z","year":"2014","publication_status":"published","publication":"Proceedings of the Annual Symposium on Computational Geometry","language":[{"iso":"eng"}],"day":"01","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0815"}],"scopus_import":1,"quality_controlled":"1","publisher":"ACM","month":"06","abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, i.e., an essential curve in the boundary of X bounding a disk in S3 nX with length bounded by a computable function of the number of tetrahedra of X."}],"acknowledgement":"ERC Advanced Grant No. 267165; Grant GRADR Eurogiga GIG/11/E023 (SNSF-PP00P2-138948); Swiss National Science Foundation (SNSF-200020-138230).","oa_version":"Submitted Version","author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"full_name":"Sedgwick, Eric","last_name":"Sedgwick","first_name":"Eric"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4849","department":[{"_id":"UlWa"}],"title":"Embeddability in the 3 sphere is decidable","citation":{"ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2014. Embeddability in the 3 sphere is decidable. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 78–84.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3 Sphere Is Decidable.” In Proceedings of the Annual Symposium on Computational Geometry, 78–84. ACM, 2014. https://doi.org/10.1145/2582112.2582137.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2014). Embeddability in the 3 sphere is decidable. In Proceedings of the Annual Symposium on Computational Geometry (pp. 78–84). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582137","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3 sphere is decidable. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:78-84. doi:10.1145/2582112.2582137","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84.","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3 sphere is decidable,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 78–84.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3 Sphere Is Decidable.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 78–84, doi:10.1145/2582112.2582137."},"date_updated":"2023-09-11T13:38:49Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2014-06-08","end_date":"2014-06-11","location":"Kyoto, Japan","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","_id":"2157"},{"publisher":"Springer Berlin Heidelberg","quality_controlled":"1","page":"137-143","date_created":"2022-03-21T07:12:16Z","doi":"10.1007/978-3-662-44199-2_24","date_published":"2014-09-01T00:00:00Z","year":"2014","publication":"ICMS 2014: International Congress on Mathematical Software","day":"01","article_processing_charge":"No","author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724"},{"first_name":"Michael","full_name":"Kerber, Michael","last_name":"Kerber"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan","last_name":"Reininghaus"},{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert"}],"title":"PHAT – Persistent Homology Algorithms Toolbox","citation":{"ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software. ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT – Persistent Homology Algorithms Toolbox.” In ICMS 2014: International Congress on Mathematical Software, 8592:137–43. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. https://doi.org/10.1007/978-3-662-44199-2_24.","apa":"Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2014). PHAT – Persistent Homology Algorithms Toolbox. In ICMS 2014: International Congress on Mathematical Software (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-662-44199-2_24","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms Toolbox. In: ICMS 2014: International Congress on Mathematical Software. Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143. doi:10.1007/978-3-662-44199-2_24","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, pp. 137–143.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology Algorithms Toolbox,” in ICMS 2014: International Congress on Mathematical Software, Seoul, South Korea, 2014, vol. 8592, pp. 137–143.","mla":"Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” ICMS 2014: International Congress on Mathematical Software, vol. 8592, Springer Berlin Heidelberg, 2014, pp. 137–43, doi:10.1007/978-3-662-44199-2_24."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 8592","place":"Berlin, Heidelberg","month":"09","abstract":[{"text":"PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations.","lang":"eng"}],"oa_version":"None","volume":8592,"related_material":{"record":[{"relation":"later_version","id":"1433","status":"public"}]},"publication_status":"published","publication_identifier":{"isbn":["9783662441985"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783662441992"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2014-08-05","end_date":"2014-08-09","location":"Seoul, South Korea","name":"ICMS: International Congress on Mathematical Software"},"type":"conference","status":"public","series_title":"LNCS","_id":"10894","department":[{"_id":"HeEd"}],"date_updated":"2023-09-20T09:42:40Z"},{"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"file_date_updated":"2020-07-14T12:46:52Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Quantitative fair simulation games","citation":{"mla":"Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST Austria, 2014, doi:10.15479/AT:IST-2014-315-v1-1.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative Fair Simulation Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-315-v1-1","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2014). Quantitative fair simulation games. IST Austria. https://doi.org/10.15479/AT:IST-2014-315-v1-1","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation Games, IST Austria, 2014.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair simulation games. IST Austria, 2014.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. Quantitative Fair Simulation Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-315-v1-1.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p."},"date_updated":"2023-09-20T12:07:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"type":"technical_report","pubrep_id":"315","status":"public","_id":"5428","page":"26","date_created":"2018-12-12T11:39:16Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"1066"}]},"date_published":"2014-12-05T00:00:00Z","doi":"10.15479/AT:IST-2014-315-v1-1","year":"2014","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5521","checksum":"b1d573bc04365625ff9974880c0aa807","creator":"system","date_updated":"2020-07-14T12:46:52Z","file_size":531046,"date_created":"2018-12-12T11:53:59Z","file_name":"IST-2014-315-v1+1_report.pdf"}],"day":"05","oa":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","month":"12","abstract":[{"text":"Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata.","lang":"eng"}],"oa_version":"Published Version"},{"page":"23 - 30","date_created":"2018-12-11T11:54:33Z","date_published":"2014-01-01T00:00:00Z","publication_status":"published","year":"2014","publication":"Zoologie","language":[{"iso":"eng"}],"day":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf"}],"publisher":"Deutsche Zoologische Gesellschaft","quality_controlled":"1","month":"01","oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5208","title":"Gemeinsame Krankheitsabwehr in Ameisengesellschaften","department":[{"_id":"SyCr"}],"citation":{"ieee":"S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” Zoologie. Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.","short":"S. Cremer, Zoologie (2014) 23–30.","apa":"Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie. Deutsche Zoologische Gesellschaft.","ama":"Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie. 2014:23-30.","mla":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie, Deutsche Zoologische Gesellschaft, 2014, pp. 23–30.","ista":"Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie., 23–30.","chicago":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” Zoologie. Deutsche Zoologische Gesellschaft, 2014."},"date_updated":"2023-10-17T07:54:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_type":"original","status":"public","_id":"1887"},{"author":[{"last_name":"Postiglione","full_name":"Postiglione, Maria P","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"publist_id":"4806","article_processing_charge":"No","title":"Monitoring neurogenesis in the cerebral cortex: an update","citation":{"mla":"Postiglione, Maria P., and Simon Hippenmeyer. “Monitoring Neurogenesis in the Cerebral Cortex: An Update.” Future Neurology, vol. 9, no. 3, Future Science Group, 2014, pp. 323–40, doi:10.2217/fnl.14.18.","short":"M.P. Postiglione, S. Hippenmeyer, Future Neurology 9 (2014) 323–340.","ieee":"M. P. Postiglione and S. Hippenmeyer, “Monitoring neurogenesis in the cerebral cortex: an update,” Future Neurology, vol. 9, no. 3. Future Science Group, pp. 323–340, 2014.","apa":"Postiglione, M. P., & Hippenmeyer, S. (2014). Monitoring neurogenesis in the cerebral cortex: an update. Future Neurology. Future Science Group. https://doi.org/10.2217/fnl.14.18","ama":"Postiglione MP, Hippenmeyer S. Monitoring neurogenesis in the cerebral cortex: an update. Future Neurology. 2014;9(3):323-340. doi:10.2217/fnl.14.18","chicago":"Postiglione, Maria P, and Simon Hippenmeyer. “Monitoring Neurogenesis in the Cerebral Cortex: An Update.” Future Neurology. Future Science Group, 2014. https://doi.org/10.2217/fnl.14.18.","ista":"Postiglione MP, Hippenmeyer S. 2014. Monitoring neurogenesis in the cerebral cortex: an update. Future Neurology. 9(3), 323–340."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"}],"page":"323 - 340","doi":"10.2217/fnl.14.18","date_published":"2014-05-01T00:00:00Z","date_created":"2018-12-11T11:56:09Z","has_accepted_license":"1","year":"2014","day":"01","publication":"Future Neurology","publisher":"Future Science Group","quality_controlled":"1","oa":1,"department":[{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:45:31Z","date_updated":"2023-10-17T08:34:27Z","ddc":["570"],"type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"528","_id":"2175","volume":9,"issue":"3","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["1479-6708"],"eissn":["1748-6971"]},"publication_status":"published","file":[{"date_created":"2018-12-12T10:10:25Z","file_name":"IST-2016-528-v1+1_fnl.14.18.pdf","creator":"system","date_updated":"2020-07-14T12:45:31Z","file_size":3848424,"checksum":"ba06659ecadabceec9a37dd8c4586dce","file_id":"4812","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 9","abstract":[{"text":"The cerebral cortex, the seat of our cognitive abilities, is composed of an intricate network of billions of excitatory projection and inhibitory interneurons. Postmitotic cortical neurons are generated by a diverse set of neural stem cell progenitors within dedicated zones and defined periods of neurogenesis during embryonic development. Disruptions in neurogenesis can lead to alterations in the neuronal cytoarchitecture, which is thought to represent a major underlying cause for several neurological disorders, including microcephaly, autism and epilepsy. Although a number of signaling pathways regulating neurogenesis have been described, the precise cellular and molecular mechanisms regulating the functional neural stem cell properties in cortical neurogenesis remain unclear. Here, we discuss the most up-to-date strategies to monitor the fundamental mechanistic parameters of neuronal progenitor proliferation, and recent advances deciphering the logic and dynamics of neurogenesis.","lang":"eng"}],"oa_version":"Published Version"},{"department":[{"_id":"CaGu"}],"date_updated":"2023-10-17T10:21:17Z","type":"journal_article","article_type":"original","status":"public","_id":"1913","volume":38,"issue":"5-6","publication_identifier":{"issn":["1420-8008"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf"}],"month":"11","intvolume":" 38","abstract":[{"text":"Deposits of phosphorylated tau protein and convergence of pathology in the hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed to evaluate whether regional and cellular vulnerability patterns in the hippocampus distinguish tauopathies or are influenced by their concomitant presence. Methods: We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal subregions/layers in individuals with Alzheimer's disease (AD)-related neurofibrillary degeneration (n = 40), Pick's disease (n = 8), progressive supranuclear palsy (n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n = 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly (n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis. Results: Our study reveals disease-specific hot spots and regional selective vulnerability for these disorders. The pattern of hippocampal AD-related tau pathology is strongly influenced by concomitant AGD. Mathematical analysis reveals that hippocampal involvement in primary tauopathies is distinguishable from early-stage AD-related neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies, which primarily do not affect the hippocampus. These hot spots can be shifted to other regions by the co-occurrence of tauopathies like AGD. Our observations support the notion that globular glial tauopathies and tau-astrogliopathy of the elderly are distinct entities.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","publist_id":"5181","author":[{"full_name":"Milenković, Ivan","last_name":"Milenković","first_name":"Ivan"},{"first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov"},{"first_name":"Gábor","full_name":"Kovács, Gábor","last_name":"Kovács"}],"external_id":{"pmid":["25195847"]},"article_processing_charge":"No","title":"Patterns of hippocampal tau pathology differentiate neurodegenerative dementias","citation":{"ama":"Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 2014;38(5-6):375-388. doi:10.1159/000365548","apa":"Milenković, I., Petrov, T., & Kovács, G. (2014). Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. Karger Publishers. https://doi.org/10.1159/000365548","short":"I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders 38 (2014) 375–388.","ieee":"I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology differentiate neurodegenerative dementias,” Dementia and Geriatric Cognitive Disorders, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.","mla":"Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders, vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:10.1159/000365548.","ista":"Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 38(5–6), 375–388.","chicago":"Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders. Karger Publishers, 2014. https://doi.org/10.1159/000365548."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"375 - 388","doi":"10.1159/000365548","date_published":"2014-11-07T00:00:00Z","date_created":"2018-12-11T11:54:41Z","year":"2014","day":"07","publication":"Dementia and Geriatric Cognitive Disorders","publisher":"Karger Publishers","quality_controlled":"1","oa":1,"acknowledgement":"This study was supported by the European Commission’s 7th Framework Programme under GA No. 278486, ‘DEVELAGE’."},{"publisher":"International Congress of Mathematicians","quality_controlled":"1","oa":1,"acknowledgement":"The author is partially supported by SFB-TR 12 Grant of the German Research Council.","date_published":"2014-08-01T00:00:00Z","date_created":"2018-12-11T11:52:25Z","page":"214 - 236","day":"01","publication":"Proceedings of the International Congress of Mathematicians","year":"2014","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Random matrices, log-gases and Hölder regularity","publist_id":"5670","author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” Proceedings of the International Congress of Mathematicians, vol. 3, International Congress of Mathematicians, 2014, pp. 214–36.","apa":"Erdös, L. (2014). Random matrices, log-gases and Hölder regularity. In Proceedings of the International Congress of Mathematicians (Vol. 3, pp. 214–236). Seoul, Korea: International Congress of Mathematicians.","ama":"Erdös L. Random matrices, log-gases and Hölder regularity. In: Proceedings of the International Congress of Mathematicians. Vol 3. International Congress of Mathematicians; 2014:214-236.","short":"L. Erdös, in:, Proceedings of the International Congress of Mathematicians, International Congress of Mathematicians, 2014, pp. 214–236.","ieee":"L. Erdös, “Random matrices, log-gases and Hölder regularity,” in Proceedings of the International Congress of Mathematicians, Seoul, Korea, 2014, vol. 3, pp. 214–236.","chicago":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” In Proceedings of the International Congress of Mathematicians, 3:214–36. International Congress of Mathematicians, 2014.","ista":"Erdös L. 2014. Random matrices, log-gases and Hölder regularity. Proceedings of the International Congress of Mathematicians. ICM: International Congress of Mathematicians vol. 3, 214–236."},"month":"08","intvolume":" 3","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1407.5752","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large real and complex Hermitian matrices with independent, identically distributed entries are universal in a sense that they depend only on the symmetry class of the matrix and otherwise are independent of the details of the distribution. We present the recent solution to this half-century old conjecture. We explain how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also show related results for log-gases that represent a universal model for strongly correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss the extensions of these universality results to more realistic physical systems such as random band matrices.","lang":"eng"}],"volume":3,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"conference","conference":{"name":"ICM: International Congress of Mathematicians","start_date":"2014-08-13","end_date":"2014-08-21","location":"Seoul, Korea"},"_id":"1507","department":[{"_id":"LaEr"}],"date_updated":"2023-10-17T11:12:55Z"},{"_id":"8044","conference":{"name":"ICM: International Congress of Mathematicans","start_date":"2014-08-13","location":"Seoul, South Korea","end_date":"2014-08-21"},"type":"conference","status":"public","date_updated":"2023-10-17T11:12:33Z","citation":{"mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” Proceeding of the International Congress of Mathematicans, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in Proceeding of the International Congress of Mathematicans, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.","ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: Proceeding of the International Congress of Mathematicans. Vol 3. International Congress of Mathematicians; 2014:1175-1194.","apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In Proceeding of the International Congress of Mathematicans (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In Proceeding of the International Congress of Mathematicans, 3:1175–94. International Congress of Mathematicians, 2014.","ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"title":"Structure of the excitation spectrum for many-body quantum systems","department":[{"_id":"RoSe"}],"abstract":[{"lang":"eng","text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system."}],"oa_version":"Published Version","main_file_link":[{"url":"http://www.icm2014.org/en/vod/proceedings.html","open_access":"1"}],"oa":1,"scopus_import":"1","quality_controlled":"1","publisher":"International Congress of Mathematicians","intvolume":" 3","month":"08","publication_status":"published","year":"2014","publication_identifier":{"isbn":["9788961058063"]},"language":[{"iso":"eng"}],"publication":"Proceeding of the International Congress of Mathematicans","day":"01","page":"1175-1194","date_created":"2020-06-29T07:59:35Z","volume":3,"date_published":"2014-08-01T00:00:00Z"},{"language":[{"iso":"eng"}],"day":"10","publication_status":"published","year":"2014","date_created":"2018-12-11T11:56:03Z","volume":32,"date_published":"2014-05-10T00:00:00Z","page":"991 - 999","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Transfer learning has received a lot of attention in the machine learning community over the last years, and several effective algorithms have been developed. However, relatively little is known about their theoretical properties, especially in the setting of lifelong learning, where the goal is to transfer information to tasks for which no data have been observed so far. In this work we study lifelong learning from a theoretical perspective. Our main result is a PAC-Bayesian generalization bound that offers a unified view on existing paradigms for transfer learning, such as the transfer of parameters or the transfer of low-dimensional representations. We also use the bound to derive two principled lifelong learning algorithms, and we show that these yield results comparable with existing methods."}],"intvolume":" 32","month":"05","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/citation.cfm?id=3045003"}],"oa":1,"quality_controlled":"1","scopus_import":"1","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Pentina and C. Lampert, “A PAC-Bayesian bound for Lifelong Learning,” presented at the ICML: International Conference on Machine Learning, Beijing, China, 2014, vol. 32, pp. 991–999.","short":"A. Pentina, C. Lampert, in:, ML Research Press, 2014, pp. 991–999.","apa":"Pentina, A., & Lampert, C. (2014). A PAC-Bayesian bound for Lifelong Learning (Vol. 32, pp. 991–999). Presented at the ICML: International Conference on Machine Learning, Beijing, China: ML Research Press.","ama":"Pentina A, Lampert C. A PAC-Bayesian bound for Lifelong Learning. In: Vol 32. ML Research Press; 2014:991-999.","mla":"Pentina, Anastasia, and Christoph Lampert. A PAC-Bayesian Bound for Lifelong Learning. Vol. 32, ML Research Press, 2014, pp. 991–99.","ista":"Pentina A, Lampert C. 2014. A PAC-Bayesian bound for Lifelong Learning. ICML: International Conference on Machine Learning vol. 32, 991–999.","chicago":"Pentina, Anastasia, and Christoph Lampert. “A PAC-Bayesian Bound for Lifelong Learning,” 32:991–99. ML Research Press, 2014."},"date_updated":"2023-10-17T11:54:24Z","department":[{"_id":"ChLa"}],"title":"A PAC-Bayesian bound for Lifelong Learning","article_processing_charge":"No","publist_id":"4844","author":[{"last_name":"Pentina","full_name":"Pentina, Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"_id":"2160","status":"public","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2014-06-21","location":"Beijing, China","end_date":"2014-06-26"},"type":"conference"},{"month":"08","alternative_title":["IST Austria Thesis"],"publisher":"IST Austria","oa_version":"None","abstract":[{"lang":"eng","text":"A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis."}],"acknowledged_ssus":[{"_id":"SSU"}],"date_published":"2014-08-01T00:00:00Z","related_material":{"record":[{"id":"2282","status":"public","relation":"part_of_dissertation"},{"id":"2950","status":"public","relation":"part_of_dissertation"},{"id":"3373","status":"public","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T11:51:49Z","page":"91","day":"01","language":[{"iso":"eng"}],"year":"2014","publication_status":"published","status":"public","type":"dissertation","_id":"1403","title":"Forces driving epithelial spreading in zebrafish epiboly","department":[{"_id":"CaHe"}],"publist_id":"5804","author":[{"full_name":"Behrndt, Martin","last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"date_updated":"2023-10-17T12:16:58Z","citation":{"chicago":"Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.” IST Austria, 2014.","ista":"Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly. IST Austria.","mla":"Behrndt, Martin. Forces Driving Epithelial Spreading in Zebrafish Epiboly. IST Austria, 2014.","short":"M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST Austria, 2014.","ieee":"M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST Austria, 2014.","ama":"Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.","apa":"Behrndt, M. (2014). Forces driving epithelial spreading in zebrafish epiboly. IST Austria."}},{"date_created":"2018-12-11T11:54:33Z","volume":43,"date_published":"2014-01-01T00:00:00Z","page":"65 - 72","publication":"Soziale Insekten in einer sich wandelnden Welt","language":[{"iso":"eng"}],"day":"01","year":"2014","publication_status":"published","publication_identifier":{"issn":["2366-2875"]},"intvolume":" 43","month":"01","publisher":"Verlag Dr. Friedrich Pfeil","quality_controlled":"1","alternative_title":["Rundgespräche der Kommission für Ökologie"],"oa_version":"None","abstract":[{"text":"Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig? Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen ergänzt werden.","lang":"ger"}],"department":[{"_id":"SyCr"}],"title":"Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften","article_processing_charge":"No","publist_id":"5207","author":[{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T12:28:45Z","citation":{"ieee":"S. Cremer, “Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften,” in Soziale Insekten in einer sich wandelnden Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","short":"S. Cremer, in:, Soziale Insekten in Einer Sich Wandelnden Welt, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","ama":"Cremer S. Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften. In: Soziale Insekten in Einer Sich Wandelnden Welt. Vol 43. Verlag Dr. Friedrich Pfeil; 2014:65-72.","apa":"Cremer, S. (2014). Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften. In Soziale Insekten in einer sich wandelnden Welt (Vol. 43, pp. 65–72). Verlag Dr. Friedrich Pfeil.","mla":"Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt Bayerische Akademie Der Wissenschaften.” Soziale Insekten in Einer Sich Wandelnden Welt, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","ista":"Cremer S. 2014.Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften. In: Soziale Insekten in einer sich wandelnden Welt. Rundgespräche der Kommission für Ökologie, vol. 43, 65–72.","chicago":"Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt Bayerische Akademie Der Wissenschaften.” In Soziale Insekten in Einer Sich Wandelnden Welt, 43:65–72. Verlag Dr. Friedrich Pfeil, 2014."},"status":"public","type":"book_chapter","_id":"1888"},{"abstract":[{"lang":"eng","text":"The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice."}],"acknowledgement":"We thank Herbert Edelsbrunner for his valuable discussions and ideas on the topic of this paper. The second author has been supported by the Max Planck Center for Visual Computing and Communication","oa_version":"Submitted Version","oa":1,"main_file_link":[{"open_access":"1","url":"http://cccg.ca/proceedings/2014/papers/paper23.pdf"}],"month":"01","year":"2014","publication_status":"submitted","publication":"arXiv","language":[{"iso":"eng"}],"day":"01","date_created":"2018-12-11T11:55:12Z","date_published":"2014-01-01T00:00:00Z","doi":"10.48550/arXiv.1401.0468","_id":"2012","article_number":"1401.0468","type":"preprint","status":"public","date_updated":"2023-10-18T08:06:45Z","citation":{"ama":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv. doi:10.48550/arXiv.1401.0468","apa":"Iglesias Ham, M., Kerber, M., & Uhler, C. (n.d.). Sphere packing with limited overlap. arXiv. https://doi.org/10.48550/arXiv.1401.0468","short":"M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.).","ieee":"M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,” arXiv. .","mla":"Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” ArXiv, 1401.0468, doi:10.48550/arXiv.1401.0468.","ista":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv, 1401.0468.","chicago":"Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing with Limited Overlap.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1401.0468."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1401.0468"]},"article_processing_charge":"No","publist_id":"5064","author":[{"last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel"},{"first_name":"Michael","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber"},{"orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"}],"department":[{"_id":"HeEd"},{"_id":"CaUh"}],"title":"Sphere packing with limited overlap"},{"oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2014","publication":"Angewandte Chemie International Edition","day":"17","page":"12949-12954","date_created":"2023-09-06T12:51:14Z","date_published":"2014-11-17T00:00:00Z","doi":"10.1002/ange.201405991","citation":{"ista":"Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 126(47), 12949–12954.","chicago":"Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/ange.201405991.","ieee":"E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable preparation of pure and dense DNA origami solutions,” Angewandte Chemie International Edition, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014.","short":"E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International Edition 126 (2014) 12949–12954.","ama":"Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 2014;126(47):12949-12954. doi:10.1002/ange.201405991","apa":"Stahl, E., Martin, T., Praetorius, F. M., & Dietz, H. (2014). Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/ange.201405991","mla":"Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition, vol. 126, no. 47, Wiley, 2014, pp. 12949–54, doi:10.1002/ange.201405991."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25346175"]},"article_processing_charge":"No","author":[{"first_name":"Evi","last_name":"Stahl","full_name":"Stahl, Evi"},{"first_name":"Thomas","full_name":"Martin, Thomas","last_name":"Martin"},{"first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","full_name":"Praetorius, Florian M"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"}],"title":"Facile and scalable preparation of pure and dense DNA origami solutions","abstract":[{"text":"DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1002/ange.201405991","open_access":"1"}],"scopus_import":"1","intvolume":" 126","month":"11","publication_status":"published","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"language":[{"iso":"eng"}],"volume":126,"issue":"47","_id":"14301","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-11-07T12:14:30Z","extern":"1"},{"intvolume":" 28","month":"10","quality_controlled":"1","publisher":"Elsevier","oa_version":"None","date_created":"2020-04-30T10:35:39Z","volume":28,"issue":"10","doi":"10.1016/j.conb.2014.06.006","date_published":"2014-10-01T00:00:00Z","page":"34-41","publication":"Current Opinion in Neurobiology","language":[{"iso":"eng"}],"day":"01","year":"2014","publication_status":"published","publication_identifier":{"issn":["0959-4388"]},"status":"public","type":"journal_article","article_type":"original","_id":"7699","title":"Harnessing vocal patterns for social communication","article_processing_charge":"No","author":[{"last_name":"Sweeney","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger"},{"full_name":"Kelley, Darcy B","last_name":"Kelley","first_name":"Darcy B"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2024-01-31T10:14:08Z","citation":{"short":"L.B. Sweeney, D.B. Kelley, Current Opinion in Neurobiology 28 (2014) 34–41.","ieee":"L. B. Sweeney and D. B. Kelley, “Harnessing vocal patterns for social communication,” Current Opinion in Neurobiology, vol. 28, no. 10. Elsevier, pp. 34–41, 2014.","apa":"Sweeney, L. B., & Kelley, D. B. (2014). Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2014.06.006","ama":"Sweeney LB, Kelley DB. Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. 2014;28(10):34-41. doi:10.1016/j.conb.2014.06.006","mla":"Sweeney, Lora B., and Darcy B. Kelley. “Harnessing Vocal Patterns for Social Communication.” Current Opinion in Neurobiology, vol. 28, no. 10, Elsevier, 2014, pp. 34–41, doi:10.1016/j.conb.2014.06.006.","ista":"Sweeney LB, Kelley DB. 2014. Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. 28(10), 34–41.","chicago":"Sweeney, Lora B., and Darcy B Kelley. “Harnessing Vocal Patterns for Social Communication.” Current Opinion in Neurobiology. Elsevier, 2014. https://doi.org/10.1016/j.conb.2014.06.006."}},{"status":"public","article_type":"original","type":"journal_article","_id":"2281","department":[{"_id":"RoSe"}],"date_updated":"2024-02-14T12:19:42Z","intvolume":" 104","month":"02","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1301.5682"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential."}],"volume":104,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","title":"On the mass concentration for Bose-Einstein condensates with attractive interactions","article_processing_charge":"No","external_id":{"arxiv":["1301.5682"]},"publist_id":"4653","author":[{"first_name":"Yujin","last_name":"Guo","full_name":"Guo, Yujin"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Guo Y, Seiringer R. On the mass concentration for Bose-Einstein condensates with attractive interactions. Letters in Mathematical Physics. 2014;104(2):141-156. doi:10.1007/s11005-013-0667-9","apa":"Guo, Y., & Seiringer, R. (2014). On the mass concentration for Bose-Einstein condensates with attractive interactions. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-013-0667-9","ieee":"Y. Guo and R. Seiringer, “On the mass concentration for Bose-Einstein condensates with attractive interactions,” Letters in Mathematical Physics, vol. 104, no. 2. Springer, pp. 141–156, 2014.","short":"Y. Guo, R. Seiringer, Letters in Mathematical Physics 104 (2014) 141–156.","mla":"Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein Condensates with Attractive Interactions.” Letters in Mathematical Physics, vol. 104, no. 2, Springer, 2014, pp. 141–56, doi:10.1007/s11005-013-0667-9.","ista":"Guo Y, Seiringer R. 2014. On the mass concentration for Bose-Einstein condensates with attractive interactions. Letters in Mathematical Physics. 104(2), 141–156.","chicago":"Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein Condensates with Attractive Interactions.” Letters in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s11005-013-0667-9."},"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:56:44Z","date_published":"2014-02-01T00:00:00Z","doi":"10.1007/s11005-013-0667-9","page":"141 - 156","publication":"Letters in Mathematical Physics","day":"01","year":"2014"},{"issue":"1","volume":10,"related_material":{"record":[{"id":"5562","status":"public","relation":"popular_science"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"c720222c5e924a4acb17f23b9381a6ca","file_id":"4965","file_size":2194790,"date_updated":"2020-07-14T12:45:35Z","creator":"system","file_name":"IST-2016-436-v1+1_journal.pcbi.1003408.pdf","date_created":"2018-12-12T10:12:46Z"}],"publication_status":"published","publication_identifier":{"issn":["1553734X"]},"intvolume":" 10","month":"01","main_file_link":[{"open_access":"1","url":"http://repository.ist.ac.at/id/eprint/436"}],"scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:35Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2024-02-21T13:46:14Z","pubrep_id":"436","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"2257","date_created":"2018-12-11T11:56:36Z","doi":"10.1371/journal.pcbi.1003408","date_published":"2014-01-02T00:00:00Z","publication":"PLoS Computational Biology","day":"02","year":"2014","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"\r\n\r\n\r\n\r\nThis work was funded by NSF grant IIS-0613435, NSF grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508, the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation, ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES: ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651.","title":"Searching for collective behavior in a large network of sensory neurons","author":[{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"first_name":"Dario","last_name":"Amodei","full_name":"Amodei, Dario"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"},{"last_name":"Berry","full_name":"Berry, Michael","first_name":"Michael"}],"publist_id":"4689","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 10(1), e1003408.","chicago":"Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003408.","apa":"Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2014). Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003408","ama":"Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for collective behavior in a large network of sensory neurons. PLoS Computational Biology. 2014;10(1). doi:10.1371/journal.pcbi.1003408","ieee":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching for collective behavior in a large network of sensory neurons,” PLoS Computational Biology, vol. 10, no. 1. Public Library of Science, 2014.","short":"G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS Computational Biology 10 (2014).","mla":"Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408."},"article_number":"e1003408"},{"publication_identifier":{"eissn":["1520-6904"],"issn":["0022-3263"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"15","volume":79,"abstract":[{"text":"The copper-catalyzed diboration of ketones followed by an acid-catalyzed elimination leads to the formation of 1,1-disubstituted and trisubstituted vinyl boronate esters with moderate to good yields and selectivity. Addition of tosic acid to the crude diboration products provides the corresponding vinyl boronate esters upon elimination. The trisubstituted vinyl boronate esters are formed as the (Z)-olefin isomer, which was established by subjecting the products to a Suzuki–Miyaura coupling reaction to obtain alkenes of known geometry.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jo500773t"}],"month":"06","intvolume":" 79","date_updated":"2024-03-25T11:50:01Z","extern":"1","_id":"15161","article_type":"letter_note","type":"journal_article","status":"public","keyword":["Organic Chemistry"],"year":"2014","day":"10","publication":"The Journal of Organic Chemistry","page":"7199-7204","doi":"10.1021/jo500773t","date_published":"2014-06-10T00:00:00Z","date_created":"2024-03-21T07:58:31Z","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"citation":{"chicago":"Guan, Weiye, Alicia K. Michael, Melissa L. McIntosh, Liza Koren-Selfridge, John P. Scott, and Timothy B. Clark. “Stereoselective Formation of Trisubstituted Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” The Journal of Organic Chemistry. American Chemical Society, 2014. https://doi.org/10.1021/jo500773t.","ista":"Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. 2014. Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. 79(15), 7199–7204.","mla":"Guan, Weiye, et al. “Stereoselective Formation of Trisubstituted Vinyl Boronate Esters by the Acid-Mediated Elimination of α-Hydroxyboronate Esters.” The Journal of Organic Chemistry, vol. 79, no. 15, American Chemical Society, 2014, pp. 7199–204, doi:10.1021/jo500773t.","apa":"Guan, W., Michael, A. K., McIntosh, M. L., Koren-Selfridge, L., Scott, J. P., & Clark, T. B. (2014). Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/jo500773t","ama":"Guan W, Michael AK, McIntosh ML, Koren-Selfridge L, Scott JP, Clark TB. Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. The Journal of Organic Chemistry. 2014;79(15):7199-7204. doi:10.1021/jo500773t","short":"W. Guan, A.K. Michael, M.L. McIntosh, L. Koren-Selfridge, J.P. Scott, T.B. Clark, The Journal of Organic Chemistry 79 (2014) 7199–7204.","ieee":"W. Guan, A. K. Michael, M. L. McIntosh, L. Koren-Selfridge, J. P. Scott, and T. B. Clark, “Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters,” The Journal of Organic Chemistry, vol. 79, no. 15. American Chemical Society, pp. 7199–7204, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Weiye","full_name":"Guan, Weiye","last_name":"Guan"},{"last_name":"Michael","full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen"},{"first_name":"Melissa L.","last_name":"McIntosh","full_name":"McIntosh, Melissa L."},{"full_name":"Koren-Selfridge, Liza","last_name":"Koren-Selfridge","first_name":"Liza"},{"first_name":"John P.","full_name":"Scott, John P.","last_name":"Scott"},{"first_name":"Timothy B.","full_name":"Clark, Timothy B.","last_name":"Clark"}],"article_processing_charge":"No","title":"Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters"},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"1","related_material":{"record":[{"id":"6383","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"6435"}]},"volume":5,"oa_version":"None","abstract":[{"text":"Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses.","lang":"eng"}],"intvolume":" 5","month":"11","scopus_import":1,"date_updated":"2024-03-27T23:30:06Z","department":[{"_id":"SyCr"}],"_id":"1999","status":"public","type":"journal_article","publication":"Current Opinion in Insect Science","day":"01","year":"2014","date_created":"2018-12-11T11:55:08Z","doi":"10.1016/j.cois.2014.09.001","date_published":"2014-11-01T00:00:00Z","page":"1 - 15","quality_controlled":"1","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science. Elsevier, 2014. https://doi.org/10.1016/j.cois.2014.09.001.","ista":"Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15.","mla":"Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:10.1016/j.cois.2014.09.001.","short":"N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15.","ieee":"N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” Current Opinion in Insect Science, vol. 5, no. 1. Elsevier, pp. 1–15, 2014.","ama":"Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. Current Opinion in Insect Science. 2014;5(1):1-15. doi:10.1016/j.cois.2014.09.001","apa":"Stroeymeyt, N., Casillas Perez, B. E., & Cremer, S. (2014). Organisational immunity in social insects. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2014.09.001"},"title":"Organisational immunity in social insects","publist_id":"5080","author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"}]},{"_id":"10384","article_type":"original","type":"journal_article","status":"public","keyword":["general physics and astronomy"],"date_updated":"2021-11-29T14:05:19Z","extern":"1","abstract":[{"text":"Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.","lang":"eng"}],"pmid":1,"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.4681"}],"month":"12","intvolume":" 111","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"24","volume":111,"article_number":"245702","citation":{"ista":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. 2013. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 111(24), 245702.","chicago":"Mognetti, B. M., Anđela Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/physrevlett.111.245702.","ama":"Mognetti BM, Šarić A, Angioletti-Uberti S, Cacciuto A, Valeriani C, Frenkel D. Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. 2013;111(24). doi:10.1103/physrevlett.111.245702","apa":"Mognetti, B. M., Šarić, A., Angioletti-Uberti, S., Cacciuto, A., Valeriani, C., & Frenkel, D. (2013). Living clusters and crystals from low-density suspensions of active colloids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.111.245702","short":"B.M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, D. Frenkel, Physical Review Letters 111 (2013).","ieee":"B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel, “Living clusters and crystals from low-density suspensions of active colloids,” Physical Review Letters, vol. 111, no. 24. American Physical Society, 2013.","mla":"Mognetti, B. M., et al. “Living Clusters and Crystals from Low-Density Suspensions of Active Colloids.” Physical Review Letters, vol. 111, no. 24, 245702, American Physical Society, 2013, doi:10.1103/physrevlett.111.245702."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Mognetti, B. M.","last_name":"Mognetti","first_name":"B. M."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"S.","last_name":"Angioletti-Uberti","full_name":"Angioletti-Uberti, S."},{"first_name":"A.","full_name":"Cacciuto, A.","last_name":"Cacciuto"},{"full_name":"Valeriani, C.","last_name":"Valeriani","first_name":"C."},{"first_name":"D.","last_name":"Frenkel","full_name":"Frenkel, D."}],"external_id":{"pmid":["24483677"],"arxiv":["1311.4681"]},"article_processing_charge":"No","title":"Living clusters and crystals from low-density suspensions of active colloids","acknowledgement":"This work was supported by the ERC Advanced Grant 227758, the National Science Foundation under Career Grant No. DMR-0846426, the Wolfson Merit Award 2007/R3 of the Royal Society of London and the EPSRC Programme Grant EP/I001352/1. BMM acknowledge T. Curk and A. Ballard for useful discussions. C. V. acknowledges financial support from a Juan de la Cierva Fellowship, from the Marie Curie Integration Grant PCIG-GA-2011-303941 ANISOKINEQ, and from the National Project FIS2010- 16159. S. A-U acknowledges support from the Alexander von Humboldt Foundation.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"year":"2013","day":"11","publication":"Physical Review Letters","date_published":"2013-12-11T00:00:00Z","doi":"10.1103/physrevlett.111.245702","date_created":"2021-11-29T13:29:31Z"},{"publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"language":[{"iso":"eng"}],"volume":9,"issue":"29","abstract":[{"text":"In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface.","lang":"eng"}],"oa_version":"None","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d"}],"scopus_import":"1","intvolume":" 9","month":"05","date_updated":"2021-11-29T14:29:31Z","extern":"1","_id":"10386","type":"journal_article","article_type":"original","keyword":["condensed matter physics","general chemistry"],"status":"public","year":"2013","publication":"Soft Matter","day":"03","date_created":"2021-11-29T14:06:32Z","doi":"10.1039/c3sm50188d","date_published":"2013-05-03T00:00:00Z","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions on the subject.","publisher":"Royal Society of Chemistry","quality_controlled":"1","citation":{"ista":"Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm50188d.","ama":"Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 2013;9(29). doi:10.1039/c3sm50188d","apa":"Šarić, A., & Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm50188d","ieee":"A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” Soft Matter, vol. 9, no. 29. Royal Society of Chemistry, 2013.","short":"A. Šarić, A. Cacciuto, Soft Matter 9 (2013).","mla":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” Soft Matter, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:10.1039/c3sm50188d."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Angelo","last_name":"Cacciuto","full_name":"Cacciuto, Angelo"}],"title":"Self-assembly of nanoparticles adsorbed on fluid and elastic membranes","article_number":"6677"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886.","chicago":"Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51495a.","ama":"Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. Soft Matter. 2013;9(37):8881-8886. doi:10.1039/c3sm51495a","apa":"Napoli, J. A., Šarić, A., & Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51495a","short":"J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.","ieee":"J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” Soft Matter, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013.","mla":"Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” Soft Matter, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:10.1039/c3sm51495a."},"title":"Collapsing nanoparticle-laden nanotubes","author":[{"first_name":"Joseph A.","full_name":"Napoli, Joseph A.","last_name":"Napoli"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Cacciuto","full_name":"Cacciuto, Angelo","first_name":"Angelo"}],"article_processing_charge":"No","acknowledgement":"This work was supported by the National Science Foundation under Career Grant no. DMR-0846426.","publisher":"Royal Society of Chemistry","quality_controlled":"1","day":"08","publication":"Soft Matter","year":"2013","doi":"10.1039/c3sm51495a","date_published":"2013-08-08T00:00:00Z","date_created":"2021-11-29T13:31:24Z","page":"8881-8886","_id":"10385","status":"public","keyword":["condensed matter physics","general chemistry"],"type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-11-29T14:05:23Z","oa_version":"None","abstract":[{"lang":"eng","text":"We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials."}],"month":"08","intvolume":" 9","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"publication_status":"published","issue":"37","volume":9},{"has_accepted_license":"1","year":"2013","day":"01","publication":"Biomedical Engineering / Biomedizinische Technik","date_published":"2013-08-01T00:00:00Z","doi":"10.1515/bmt-2013-4181","date_created":"2021-12-01T14:35:35Z","publisher":"De Gruyter","quality_controlled":"1","oa":1,"citation":{"chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.","mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181","apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter. https://doi.org/10.1515/bmt-2013-4181","ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” Biomedical Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013)."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"full_name":"Schmidt-Hieber, C.","last_name":"Schmidt-Hieber","first_name":"C."},{"last_name":"Guzman","full_name":"Guzman, S. J.","first_name":"S. J."}],"external_id":{"pmid":["24042795"]},"article_processing_charge":"No","title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","article_number":"000010151520134181","publication_identifier":{"eissn":["1862-278X"],"issn":["0013-5585"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"cdfc5339b530a25d6079f7223f0b1f16","file_id":"10397","success":1,"creator":"schloegl","date_updated":"2021-12-01T14:38:08Z","file_size":149825,"date_created":"2021-12-01T14:38:08Z","file_name":"Schloegl_Abstract-BMT2013.pdf"}],"language":[{"iso":"eng"}],"issue":"SI-1-Track-G","volume":58,"abstract":[{"text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"month":"08","intvolume":" 58","date_updated":"2021-12-02T12:51:12Z","ddc":["005","610"],"file_date_updated":"2021-12-01T14:38:08Z","department":[{"_id":"PeJo"}],"_id":"10396","article_type":"original","type":"journal_article","conference":{"name":"BMT: Biomedizinische Technik ","location":"Graz, Austria","end_date":"2013-09-21","start_date":"2013-09-19"},"status":"public","keyword":["biomedical engineering","data analysis","free software"]},{"abstract":[{"lang":"eng","text":"Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures."}],"oa_version":"Published Version","alternative_title":["Bulletin of the American Physical Society"],"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR13/Event/186873","open_access":"1"}],"month":"03","intvolume":" 58","publication_identifier":{"issn":["0003-0503"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":58,"issue":"1","_id":"10749","type":"conference","conference":{"location":"Baltimore, MD, United States","end_date":"2013-03-22","start_date":"2013-03-18","name":"APS: American Physical Society"},"status":"public","date_updated":"2022-02-08T10:48:06Z","extern":"1","acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the US DOE, Office of Science.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"year":"2013","day":"01","publication":"APS March Meeting 2013","date_published":"2013-03-01T00:00:00Z","date_created":"2022-02-08T10:34:29Z","article_number":"N36.00001","citation":{"mla":"Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” APS March Meeting 2013, vol. 58, no. 1, N36.00001, American Physical Society, 2013.","short":"H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical Society, 2013.","ieee":"H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic Bi2212 samples,” in APS March Meeting 2013, Baltimore, MD, United States, 2013, vol. 58, no. 1.","ama":"Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In: APS March Meeting 2013. Vol 58. American Physical Society; 2013.","apa":"Polshyn, H., Budakian, R., & Gu, G. (2013). Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In APS March Meeting 2013 (Vol. 58). Baltimore, MD, United States: American Physical Society.","chicago":"Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” In APS March Meeting 2013, Vol. 58. American Physical Society, 2013.","ista":"Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin of the American Physical Society, vol. 58, N36.00001."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn"},{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"},{"full_name":"Gu, Genda","last_name":"Gu","first_name":"Genda"}],"article_processing_charge":"No","title":"Cantilever micro-susceptometry of mesoscopic Bi2212 samples"},{"ddc":["580"],"date_updated":"2022-03-21T12:15:29Z","file_date_updated":"2022-03-21T12:12:56Z","department":[{"_id":"JiFr"}],"_id":"10895","keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"status":"public","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_size":670188,"date_updated":"2022-03-21T12:12:56Z","creator":"dernst","file_name":"2013_Plants_Vanneste.pdf","date_created":"2022-03-21T12:12:56Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10916","checksum":"fb4ff2e820e344e253c9197544610be6"}],"publication_status":"published","publication_identifier":{"issn":["2223-7747"]},"license":"https://creativecommons.org/licenses/by/3.0/","volume":2,"issue":"4","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. ","lang":"eng"}],"intvolume":" 2","month":"10","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.","apa":"Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action. Plants. MDPI. https://doi.org/10.3390/plants2040650","ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants. 2013;2(4):650-675. doi:10.3390/plants2040650","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants, vol. 2, no. 4. MDPI, pp. 650–675, 2013."},"title":"Calcium: The missing link in auxin action","external_id":{"pmid":["27137397"]},"article_processing_charge":"No","author":[{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"Plants","day":"21","year":"2013","has_accepted_license":"1","date_created":"2022-03-21T07:13:49Z","date_published":"2013-10-21T00:00:00Z","doi":"10.3390/plants2040650","page":"650-675","oa":1,"publisher":"MDPI","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered."}],"oa_version":"None","publisher":"ACM Press","quality_controlled":"1","scopus_import":"1","month":"05","year":"2013","publication_status":"published","publication_identifier":{"isbn":["978-145032053-5"]},"publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","language":[{"iso":"eng"}],"day":"01","date_created":"2022-03-21T07:33:22Z","doi":"10.1145/2482767.2482789","date_published":"2013-05-01T00:00:00Z","issue":"5","_id":"10898","article_number":"17","conference":{"start_date":"2013-05-14","end_date":"2013-05-16","location":"Ischia, Italy","name":"CF: Conference on Computing Frontiers"},"type":"conference","status":"public","date_updated":"2022-06-21T08:01:19Z","citation":{"ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. ACM Press, 2013. https://doi.org/10.1145/2482767.2482789.","short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM Press, 2013.","ieee":"A. Haas et al., “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, Ischia, Italy, 2013, no. 5.","apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., & Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. Ischia, Italy: ACM Press. https://doi.org/10.1145/2482767.2482789","ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. ACM Press; 2013. doi:10.1145/2482767.2482789","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, no. 5, 17, ACM Press, 2013, doi:10.1145/2482767.2482789."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"full_name":"Lippautz, Michael","last_name":"Lippautz","first_name":"Michael"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Payer","full_name":"Payer, Hannes","first_name":"Hannes"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"},{"first_name":"Christoph M.","full_name":"Kirsch, Christoph M.","last_name":"Kirsch"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali"}],"title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","department":[{"_id":"ToHe"}]},{"oa_version":"None","month":"01","scopus_import":"1","quality_controlled":"1","publisher":"Elsevier","edition":"2","day":"01","language":[{"iso":"eng"}],"publication":"Encyclopedia of Biodiversity","publication_identifier":{"isbn":["978-0-12-384720-1"]},"year":"2013","publication_status":"published","date_published":"2013-01-01T00:00:00Z","doi":"10.1016/b978-0-12-384719-5.00031-9","date_created":"2022-03-21T07:46:22Z","page":"508-515","_id":"10899","status":"public","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-06-20T09:18:06Z","citation":{"ama":"Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed. Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9","apa":"Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity (2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9","ieee":"N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","mla":"Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9.","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","chicago":"Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity, 2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9."},"title":"Differentiation","department":[{"_id":"NiBa"}],"author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"type":"journal_article","article_type":"original","keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"status":"public","_id":"11086","date_updated":"2022-07-18T08:45:58Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1003308"}],"scopus_import":"1","intvolume":" 9","month":"02","abstract":[{"lang":"eng","text":"Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs."}],"oa_version":"Published Version","pmid":1,"issue":"2","volume":9,"publication_status":"published","publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"article_number":"e1003308","article_processing_charge":"No","external_id":{"pmid":["23468646"]},"author":[{"first_name":"Yun","full_name":"Liang, Yun","last_name":"Liang"},{"first_name":"Tobias M.","last_name":"Franks","full_name":"Franks, Tobias M."},{"full_name":"Marchetto, Maria C.","last_name":"Marchetto","first_name":"Maria C."},{"first_name":"Fred H.","full_name":"Gage, Fred H.","last_name":"Gage"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"title":"Dynamic association of NUP98 with the human genome","citation":{"short":"Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics 9 (2013).","ieee":"Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic association of NUP98 with the human genome,” PLoS Genetics, vol. 9, no. 2. Public Library of Science, 2013.","apa":"Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., & Hetzer, M. (2013). Dynamic association of NUP98 with the human genome. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003308","ama":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of NUP98 with the human genome. PLoS Genetics. 2013;9(2). doi:10.1371/journal.pgen.1003308","mla":"Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003308.","ista":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308.","chicago":"Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin Hetzer. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003308."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","date_created":"2022-04-07T07:50:59Z","doi":"10.1371/journal.pgen.1003308","date_published":"2013-02-28T00:00:00Z","year":"2013","publication":"PLoS Genetics","day":"28"},{"date_updated":"2022-07-18T08:50:47Z","extern":"1","_id":"11087","type":"journal_article","article_type":"original","status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"publication_identifier":{"issn":["0092-8674"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"5","volume":154,"abstract":[{"lang":"eng","text":"Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.07.037","open_access":"1"}],"month":"08","intvolume":" 154","citation":{"ista":"Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982.","chicago":"Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037.","apa":"Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.07.037","ama":"Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982. doi:10.1016/j.cell.2013.07.037","ieee":"B. H. Toyama et al., “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” Cell, vol. 154, no. 5. Elsevier, pp. 971–982, 2013.","short":"B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982.","mla":"Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","author":[{"first_name":"Brandon H.","last_name":"Toyama","full_name":"Toyama, Brandon H."},{"last_name":"Savas","full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N."},{"last_name":"Park","full_name":"Park, Sung Kyu","first_name":"Sung Kyu"},{"first_name":"Michael S.","last_name":"Harris","full_name":"Harris, Michael S."},{"full_name":"Ingolia, Nicholas T.","last_name":"Ingolia","first_name":"Nicholas T."},{"last_name":"Yates","full_name":"Yates, John R.","first_name":"John R."},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"article_processing_charge":"No","external_id":{"pmid":["23993091"]},"title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","year":"2013","day":"29","publication":"Cell","page":"971-982","date_published":"2013-08-29T00:00:00Z","doi":"10.1016/j.cell.2013.07.037","date_created":"2022-04-07T07:51:08Z","quality_controlled":"1","publisher":"Elsevier","oa":1},{"citation":{"mla":"Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:10.1016/j.cell.2013.06.007.","ieee":"E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear envelope collapse in cancer cell micronuclei,” Cell, vol. 154, no. 1. Elsevier, pp. 47–60, 2013.","short":"E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.","ama":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 2013;154(1):47-60. doi:10.1016/j.cell.2013.06.007","apa":"Hatch, E. M., Fischer, A. H., Deerinck, T. J., & Hetzer, M. (2013). Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.06.007","chicago":"Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.06.007.","ista":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 154(1), 47–60."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_processing_charge":"No","external_id":{"pmid":["23827674"]},"author":[{"first_name":"Emily M.","last_name":"Hatch","full_name":"Hatch, Emily M."},{"full_name":"Fischer, Andrew H.","last_name":"Fischer","first_name":"Andrew H."},{"full_name":"Deerinck, Thomas J.","last_name":"Deerinck","first_name":"Thomas J."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"title":"Catastrophic nuclear envelope collapse in cancer cell micronuclei","year":"2013","publication":"Cell","day":"03","page":"47-60","date_created":"2022-04-07T07:50:51Z","date_published":"2013-07-03T00:00:00Z","doi":"10.1016/j.cell.2013.06.007","oa":1,"publisher":"Elsevier","quality_controlled":"1","date_updated":"2022-07-18T08:45:47Z","extern":"1","_id":"11085","article_type":"original","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0092-8674"]},"language":[{"iso":"eng"}],"volume":154,"issue":"1","abstract":[{"lang":"eng","text":"During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.06.007"}],"scopus_import":"1","intvolume":" 154","month":"07"},{"type":"journal_article","article_type":"original","status":"public","keyword":["Biophysics"],"_id":"11088","date_updated":"2022-07-18T08:51:01Z","extern":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.bpj.2013.01.049"}],"month":"04","intvolume":" 104","abstract":[{"lang":"eng","text":"The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM."}],"oa_version":"Published Version","pmid":1,"issue":"8","volume":104,"publication_identifier":{"issn":["0006-3495"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Benjamin M.","last_name":"Regner","full_name":"Regner, Benjamin M."},{"first_name":"Dejan","full_name":"Vučinić, Dejan","last_name":"Vučinić"},{"full_name":"Domnisoru, Cristina","last_name":"Domnisoru","first_name":"Cristina"},{"first_name":"Thomas M.","last_name":"Bartol","full_name":"Bartol, Thomas M."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"first_name":"Daniel M.","full_name":"Tartakovsky, Daniel M.","last_name":"Tartakovsky"},{"last_name":"Sejnowski","full_name":"Sejnowski, Terrence J.","first_name":"Terrence J."}],"external_id":{"pmid":["23601312"]},"article_processing_charge":"No","title":"Anomalous diffusion of single particles in cytoplasm","citation":{"short":"B.M. Regner, D. Vučinić, C. Domnisoru, T.M. Bartol, M. Hetzer, D.M. Tartakovsky, T.J. Sejnowski, Biophysical Journal 104 (2013) 1652–1660.","ieee":"B. M. Regner et al., “Anomalous diffusion of single particles in cytoplasm,” Biophysical Journal, vol. 104, no. 8. Elsevier, pp. 1652–1660, 2013.","ama":"Regner BM, Vučinić D, Domnisoru C, et al. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal. 2013;104(8):1652-1660. doi:10.1016/j.bpj.2013.01.049","apa":"Regner, B. M., Vučinić, D., Domnisoru, C., Bartol, T. M., Hetzer, M., Tartakovsky, D. M., & Sejnowski, T. J. (2013). Anomalous diffusion of single particles in cytoplasm. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2013.01.049","mla":"Regner, Benjamin M., et al. “Anomalous Diffusion of Single Particles in Cytoplasm.” Biophysical Journal, vol. 104, no. 8, Elsevier, 2013, pp. 1652–60, doi:10.1016/j.bpj.2013.01.049.","ista":"Regner BM, Vučinić D, Domnisoru C, Bartol TM, Hetzer M, Tartakovsky DM, Sejnowski TJ. 2013. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal. 104(8), 1652–1660.","chicago":"Regner, Benjamin M., Dejan Vučinić, Cristina Domnisoru, Thomas M. Bartol, Martin Hetzer, Daniel M. Tartakovsky, and Terrence J. Sejnowski. “Anomalous Diffusion of Single Particles in Cytoplasm.” Biophysical Journal. Elsevier, 2013. https://doi.org/10.1016/j.bpj.2013.01.049."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"1652-1660","date_published":"2013-04-16T00:00:00Z","doi":"10.1016/j.bpj.2013.01.049","date_created":"2022-04-07T07:51:26Z","year":"2013","day":"16","publication":"Biophysical Journal"},{"extern":"1","date_updated":"2022-07-18T08:45:34Z","_id":"11083","keyword":["Cell Biology"],"status":"public","type":"journal_article","article_type":"letter_note","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0962-8924"]},"issue":"3","volume":23,"pmid":1,"oa_version":"None","abstract":[{"text":"Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML.","lang":"eng"}],"intvolume":" 23","month":"03","scopus_import":"1","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"ista":"Franks TM, Hetzer M. 2013. The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. 23(3), 112–117.","chicago":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” Trends in Cell Biology. Elsevier, 2013. https://doi.org/10.1016/j.tcb.2012.10.013.","ama":"Franks TM, Hetzer M. The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. 2013;23(3):112-117. doi:10.1016/j.tcb.2012.10.013","apa":"Franks, T. M., & Hetzer, M. (2013). The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2012.10.013","ieee":"T. M. Franks and M. Hetzer, “The role of Nup98 in transcription regulation in healthy and diseased cells,” Trends in Cell Biology, vol. 23, no. 3. Elsevier, pp. 112–117, 2013.","short":"T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 112–117.","mla":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” Trends in Cell Biology, vol. 23, no. 3, Elsevier, 2013, pp. 112–17, doi:10.1016/j.tcb.2012.10.013."},"title":"The role of Nup98 in transcription regulation in healthy and diseased cells","article_processing_charge":"No","external_id":{"pmid":["23246429"]},"author":[{"last_name":"Franks","full_name":"Franks, Tobias M.","first_name":"Tobias M."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"publication":"Trends in Cell Biology","day":"01","year":"2013","date_created":"2022-04-07T07:50:33Z","date_published":"2013-03-01T00:00:00Z","doi":"10.1016/j.tcb.2012.10.013","page":"112-117","publisher":"Elsevier","quality_controlled":"1"},{"_id":"11084","type":"journal_article","article_type":"original","status":"public","keyword":["Cell Biology","Molecular Biology"],"date_updated":"2022-07-18T08:37:53Z","extern":"1","abstract":[{"text":"Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"01","intvolume":" 14","publication_identifier":{"issn":["1471-0072","1471-0080"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":14,"citation":{"short":"B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61.","ieee":"B. H. Toyama and M. Hetzer, “Protein homeostasis: Live long, won’t prosper,” Nature Reviews Molecular Cell Biology, vol. 14. Springer Nature, pp. 55–61, 2013.","ama":"Toyama BH, Hetzer M. Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. 2013;14:55-61. doi:10.1038/nrm3496","apa":"Toyama, B. H., & Hetzer, M. (2013). Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/nrm3496","mla":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” Nature Reviews Molecular Cell Biology, vol. 14, Springer Nature, 2013, pp. 55–61, doi:10.1038/nrm3496.","ista":"Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. 14, 55–61.","chicago":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” Nature Reviews Molecular Cell Biology. Springer Nature, 2013. https://doi.org/10.1038/nrm3496."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","author":[{"first_name":"Brandon H.","last_name":"Toyama","full_name":"Toyama, Brandon H."},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"article_processing_charge":"No","external_id":{"pmid":["23258296"]},"title":"Protein homeostasis: Live long, won't prosper","publisher":"Springer Nature","quality_controlled":"1","year":"2013","day":"01","publication":"Nature Reviews Molecular Cell Biology","page":"55-61","doi":"10.1038/nrm3496","date_published":"2013-01-01T00:00:00Z","date_created":"2022-04-07T07:50:43Z"},{"month":"02","intvolume":" 84","publisher":"AIP","quality_controlled":"1","oa_version":"None","acknowledgement":"This work was supported financially by the National Science Foundation (NSF) through its Materials Research Science and Engineering Center (MRSEC) program (DMR-0820054) and by the US Army Research Office through Grant No. W911NF-12-1-0182. S.R.W. acknowledges support from a University of Chicago Millikan Fellowship.","abstract":[{"lang":"eng","text":"We present the design and performance characterization of a new experimental technique for measuring individual particle charges in large ensembles of macroscopic grains. The measurement principle is qualitatively similar to that used in determining the elementary charge by Millikan in that it follows individual particle trajectories. However, by taking advantage of new technology we are able to work with macroscopic grains and achieve several orders of magnitude better resolution in charge to mass ratios. By observing freely falling grains accelerated in a horizontal electric field with a co-falling, high-speed video camera, we dramatically increase particle tracking time and measurement precision. Keeping the granular medium under vacuum, we eliminate air drag, leaving the electrostatic force as the primary source of particle accelerations in the co-moving frame. Because the technique is based on direct imaging, we can distinguish between different particle types during the experiment, opening up the possibility of studying charge transfer processes between different particle species. For the ∼300 μm diameter grains reported here, we achieve an average acceleration resolution of ∼0.008 m/s2, a force resolution of ∼500 pN, and a median charge resolution ∼6× 104 elementary charges per grain (corresponding to surface charge densities ∼1 elementary charges per μm2). The primary source of error is indeterminacy in the grain mass, but with higher resolution cameras and better optics this can be further improved. The high degree of resolution and the ability to visually identify particles of different species or sizes with direct imaging make this a powerful new tool to characterize charging processes in granular media."}],"doi":"10.1063/1.4789496","volume":84,"date_published":"2013-02-07T00:00:00Z","issue":"2","date_created":"2018-12-11T11:44:42Z","day":"07","language":[{"iso":"eng"}],"publication":"Review of Scientific Instruments","publication_status":"published","year":"2013","status":"public","type":"journal_article","article_number":"025104","_id":"115","title":"In situ granular charge measurement by free-fall videography","publist_id":"7939","author":[{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"},{"last_name":"Jaeger","full_name":"Jaeger, Heinrich","first_name":"Heinrich"}],"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:39Z","citation":{"chicago":"Waitukaitis, Scott R, and Heinrich Jaeger. “In Situ Granular Charge Measurement by Free-Fall Videography.” Review of Scientific Instruments. AIP, 2013. https://doi.org/10.1063/1.4789496.","ista":"Waitukaitis SR, Jaeger H. 2013. In situ granular charge measurement by free-fall videography. Review of Scientific Instruments. 84(2), 025104.","mla":"Waitukaitis, Scott R., and Heinrich Jaeger. “In Situ Granular Charge Measurement by Free-Fall Videography.” Review of Scientific Instruments, vol. 84, no. 2, 025104, AIP, 2013, doi:10.1063/1.4789496.","short":"S.R. Waitukaitis, H. Jaeger, Review of Scientific Instruments 84 (2013).","ieee":"S. R. Waitukaitis and H. Jaeger, “In situ granular charge measurement by free-fall videography,” Review of Scientific Instruments, vol. 84, no. 2. AIP, 2013.","apa":"Waitukaitis, S. R., & Jaeger, H. (2013). In situ granular charge measurement by free-fall videography. Review of Scientific Instruments. AIP. https://doi.org/10.1063/1.4789496","ama":"Waitukaitis SR, Jaeger H. In situ granular charge measurement by free-fall videography. Review of Scientific Instruments. 2013;84(2). doi:10.1063/1.4789496"}},{"article_number":"139","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"D. Sobral et al., “The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS,” The Astrophysical Journal, vol. 779, no. 2. IOP Publishing, 2013.","short":"D. Sobral, A.M. Swinbank, J.P. Stott, J.J. Matthee, R.G. Bower, I. Smail, P. Best, J.E. Geach, R.M. Sharples, The Astrophysical Journal 779 (2013).","apa":"Sobral, D., Swinbank, A. M., Stott, J. P., Matthee, J. J., Bower, R. G., Smail, I., … Sharples, R. M. (2013). The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. IOP Publishing. https://doi.org/10.1088/0004-637x/779/2/139","ama":"Sobral D, Swinbank AM, Stott JP, et al. The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. 2013;779(2). doi:10.1088/0004-637x/779/2/139","mla":"Sobral, D., et al. “The Dynamics of Z=0.8 H-Alpha-Selected Star-Forming Galaxies from KMOS/CF-HiZELS.” The Astrophysical Journal, vol. 779, no. 2, 139, IOP Publishing, 2013, doi:10.1088/0004-637x/779/2/139.","ista":"Sobral D, Swinbank AM, Stott JP, Matthee JJ, Bower RG, Smail I, Best P, Geach JE, Sharples RM. 2013. The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS. The Astrophysical Journal. 779(2), 139.","chicago":"Sobral, D., A. M. Swinbank, J. P. Stott, Jorryt J Matthee, R. G. Bower, Ian Smail, P. Best, J. E. Geach, and R. M. Sharples. “The Dynamics of Z=0.8 H-Alpha-Selected Star-Forming Galaxies from KMOS/CF-HiZELS.” The Astrophysical Journal. IOP Publishing, 2013. https://doi.org/10.1088/0004-637x/779/2/139."},"title":"The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS","article_processing_charge":"No","external_id":{"arxiv":["1310.3822"]},"author":[{"first_name":"D.","full_name":"Sobral, D.","last_name":"Sobral"},{"full_name":"Swinbank, A. M.","last_name":"Swinbank","first_name":"A. M."},{"last_name":"Stott","full_name":"Stott, J. P.","first_name":"J. P."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee"},{"full_name":"Bower, R. G.","last_name":"Bower","first_name":"R. G."},{"first_name":"Ian","full_name":"Smail, Ian","last_name":"Smail"},{"first_name":"P.","last_name":"Best","full_name":"Best, P."},{"first_name":"J. E.","last_name":"Geach","full_name":"Geach, J. E."},{"full_name":"Sharples, R. M.","last_name":"Sharples","first_name":"R. M."}],"acknowledgement":"We thank the referee for many helpful comments and suggestions which greatly improved the clarity and quality of this work. D.S. acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and also funding from the European Community Seventh Framework Programme (FP7/2007-2013) under grant agreement number RG226604 (OPTICON) which allowed access to CFHT time (proposals: 11BO29 & 12AO19). A.M.S. gratefully acknowledges an STFC Advanced Fellowship through grant number ST/H005234/1. I.R.S., J.P.S., and R.G.B. acknowledge support from the UK Science and Technology Facilities Council (STFC) under ST/I001573/1. I.R.S. acknowledges STFC (ST/J001422/1), the ERC Advanced Investigator program DUSTYGAL and a Royal Society/Wolfson Merit Award. P.N.B. acknowledges support from STFC. R.M.S. acknowledges support from the grant ST/1001573/1. The data presented here are based on observations with the KMOS spectrograph on the ESO/VLT under program 60.A-9460 and can be accessed through the ESO data archive. The authors also wish to acknowledge the help from Michael Hilker in preparing the KMOS observations.","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","publication":"The Astrophysical Journal","day":"03","year":"2013","date_created":"2022-07-07T09:14:48Z","doi":"10.1088/0004-637x/779/2/139","date_published":"2013-12-03T00:00:00Z","_id":"11520","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution – galaxies","high-redshift – galaxies","starburst"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2022-08-18T10:43:07Z","oa_version":"Preprint","abstract":[{"text":"We present the spatially resolved Hα dynamics of 16 star-forming galaxies at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc overdensity of Hα emitters and likely reside in a group/intermediate environment, but not a cluster. We confirm and identify a rich group of star-forming galaxies at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can be described by rotating disks and use the data to derive inclination corrected rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75% ± 8%, consistent with previous results based on Hubble Space Telescope morphologies of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation, confirming the evolution seen in the zero point. Apart from having, on average, higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all disk galaxies.","lang":"eng"}],"intvolume":" 779","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.3822"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"volume":779,"issue":"2"},{"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Waitukaitis SR, Roth L, Vitelli V, Jaeger H. 2013. Dynamic jamming fronts. EPL. 102(4), 44001.","chicago":"Waitukaitis, Scott R, Leah Roth, Vincenzo Vitelli, and Heinrich Jaeger. “Dynamic Jamming Fronts.” EPL. Elsevier, 2013. https://doi.org/10.1209/0295-5075/102/44001.","ama":"Waitukaitis SR, Roth L, Vitelli V, Jaeger H. Dynamic jamming fronts. EPL. 2013;102(4). doi:10.1209/0295-5075/102/44001","apa":"Waitukaitis, S. R., Roth, L., Vitelli, V., & Jaeger, H. (2013). Dynamic jamming fronts. EPL. Elsevier. https://doi.org/10.1209/0295-5075/102/44001","ieee":"S. R. Waitukaitis, L. Roth, V. Vitelli, and H. Jaeger, “Dynamic jamming fronts,” EPL, vol. 102, no. 4. Elsevier, 2013.","short":"S.R. Waitukaitis, L. Roth, V. Vitelli, H. Jaeger, EPL 102 (2013).","mla":"Waitukaitis, Scott R., et al. “Dynamic Jamming Fronts.” EPL, vol. 102, no. 4, 44001, Elsevier, 2013, doi:10.1209/0295-5075/102/44001."},"date_updated":"2021-01-12T06:48:44Z","title":"Dynamic jamming fronts","publist_id":"7938","author":[{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"},{"last_name":"Roth","full_name":"Roth, Leah","first_name":"Leah"},{"first_name":"Vincenzo","full_name":"Vitelli, Vincenzo","last_name":"Vitelli"},{"first_name":"Heinrich","last_name":"Jaeger","full_name":"Jaeger, Heinrich"}],"article_number":"44001","_id":"116","status":"public","type":"journal_article","day":"24","publication":"EPL","language":[{"iso":"eng"}],"year":"2013","publication_status":"published","issue":"4","date_published":"2013-05-24T00:00:00Z","volume":102,"doi":"10.1209/0295-5075/102/44001","date_created":"2018-12-11T11:44:43Z","oa_version":"None","acknowledgement":"This work was supported by the National Science Foundation (NSF) through its Materials Research Science and Engineering program (DMR-0820054). SRW was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-FG02-03ER46088. LKR acknowledges support through the NSF Research Experience for Undergraduates program.","abstract":[{"text":"We describe a model experiment for dynamic jamming: a two-dimensional collection of initially unjammed disks that are forced into the jammed state by uniaxial compression via a rake. This leads to a stable densification front that travels ahead of the rake, leaving regions behind it jammed. Using disk conservation in conjunction with an upper limit to the packing fraction at jamming onset, we predict the front speed as a function of packing fraction and rake speed. However, we find that the jamming front has a finite width, a feature that cannot be explained by disk conservation alone. This width appears to diverge on approach to jamming, which suggests that it may be related to growing lengthscales encountered in other jamming studies.","lang":"eng"}],"month":"05","intvolume":" 102","publisher":"Elsevier","quality_controlled":"1"},{"volume":7,"issue":"1","publication_status":"published","publication_identifier":{"issn":["1559-1131"],"eissn":["1559-114X"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 7","month":"03","abstract":[{"lang":"eng","text":"Given only the URL of a Web page, can we identify its language? In this article we examine this question. URL-based language classification is useful when the content of the Web page is not available or downloading the content is a waste of bandwidth and time.\r\nWe built URL-based language classifiers for English, German, French, Spanish, and Italian by applying a variety of algorithms and features. As algorithms we used machine learning algorithms which are widely applied for text classification and state-of-art algorithms for language identification of text. As features we used words, various sized n-grams, and custom-made features (our novel feature set). We compared our approaches with two baseline methods, namely classification by country code top-level domains and classification by IP addresses of the hosting Web servers.\r\n\r\nWe trained and tested our classifiers in a 10-fold cross-validation setup on a dataset obtained from the Open Directory Project and from querying a commercial search engine. We obtained the lowest F1-measure for English (94) and the highest F1-measure for German (98) with the best performing classifiers.\r\n\r\nWe also evaluated the performance of our methods: (i) on a set of Web pages written in Adobe Flash and (ii) as part of a language-focused crawler. In the first case, the content of the Web page is hard to extract and in the second page downloading pages of the “wrong” language constitutes a waste of bandwidth. In both settings the best classifiers have a high accuracy with an F1-measure between 95 (for English) and 98 (for Italian) for the Adobe Flash pages and a precision between 90 (for Italian) and 97 (for French) for the language-focused crawler."}],"oa_version":"None","date_updated":"2022-09-12T08:51:57Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Computer Networks and Communications"],"status":"public","_id":"11671","date_created":"2022-07-27T12:50:18Z","doi":"10.1145/2435215.2435218","date_published":"2013-03-01T00:00:00Z","year":"2013","publication":"ACM Transactions on the Web","day":"01","quality_controlled":"1","publisher":"Association for Computing Machinery","article_processing_charge":"No","author":[{"first_name":"Eda","last_name":"Baykan","full_name":"Baykan, Eda"},{"first_name":"Ingmar","last_name":"Weber","full_name":"Weber, Ingmar"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"}],"title":"A comprehensive study of techniques for URL-based web page language classification","citation":{"mla":"Baykan, Eda, et al. “A Comprehensive Study of Techniques for URL-Based Web Page Language Classification.” ACM Transactions on the Web, vol. 7, no. 1, 3, Association for Computing Machinery, 2013, doi:10.1145/2435215.2435218.","ama":"Baykan E, Weber I, Henzinger MH. A comprehensive study of techniques for URL-based web page language classification. ACM Transactions on the Web. 2013;7(1). doi:10.1145/2435215.2435218","apa":"Baykan, E., Weber, I., & Henzinger, M. H. (2013). A comprehensive study of techniques for URL-based web page language classification. ACM Transactions on the Web. Association for Computing Machinery. https://doi.org/10.1145/2435215.2435218","short":"E. Baykan, I. Weber, M.H. Henzinger, ACM Transactions on the Web 7 (2013).","ieee":"E. Baykan, I. Weber, and M. H. Henzinger, “A comprehensive study of techniques for URL-based web page language classification,” ACM Transactions on the Web, vol. 7, no. 1. Association for Computing Machinery, 2013.","chicago":"Baykan, Eda, Ingmar Weber, and Monika H Henzinger. “A Comprehensive Study of Techniques for URL-Based Web Page Language Classification.” ACM Transactions on the Web. Association for Computing Machinery, 2013. https://doi.org/10.1145/2435215.2435218.","ista":"Baykan E, Weber I, Henzinger MH. 2013. A comprehensive study of techniques for URL-based web page language classification. ACM Transactions on the Web. 7(1), 3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"3"},{"author":[{"last_name":"Jaeger","full_name":"Jaeger, Heinrich","first_name":"Heinrich"},{"first_name":"Marc","last_name":"Miskin","full_name":"Miskin, Marc"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"}],"publist_id":"7937","title":"From nanoscale cohesion to macroscale entanglement: opportunities for designing granular aggregate behaviour by tailoring grain shape and interactions","date_updated":"2021-01-12T06:48:49Z","citation":{"ista":"Jaeger H, Miskin M, Waitukaitis SR. 2013. From nanoscale cohesion to macroscale entanglement: opportunities for designing granular aggregate behaviour by tailoring grain shape and interactions. AIP Conference Proceedings. Powders and Grains vol. 1542, 3–6.","chicago":"Jaeger, Heinrich, Marc Miskin, and Scott R Waitukaitis. “From Nanoscale Cohesion to Macroscale Entanglement: Opportunities for Designing Granular Aggregate Behaviour by Tailoring Grain Shape and Interactions.” In AIP Conference Proceedings, 1542:3–6. AIP, 2013. https://doi.org/10.1063/1.4811858.","ama":"Jaeger H, Miskin M, Waitukaitis SR. From nanoscale cohesion to macroscale entanglement: opportunities for designing granular aggregate behaviour by tailoring grain shape and interactions. In: AIP Conference Proceedings. Vol 1542. AIP; 2013:3-6. doi:10.1063/1.4811858","apa":"Jaeger, H., Miskin, M., & Waitukaitis, S. R. (2013). From nanoscale cohesion to macroscale entanglement: opportunities for designing granular aggregate behaviour by tailoring grain shape and interactions. In AIP Conference Proceedings (Vol. 1542, pp. 3–6). Sydney, Australia: AIP. https://doi.org/10.1063/1.4811858","ieee":"H. Jaeger, M. Miskin, and S. R. Waitukaitis, “From nanoscale cohesion to macroscale entanglement: opportunities for designing granular aggregate behaviour by tailoring grain shape and interactions,” in AIP Conference Proceedings, Sydney, Australia, 2013, vol. 1542, pp. 3–6.","short":"H. Jaeger, M. Miskin, S.R. Waitukaitis, in:, AIP Conference Proceedings, AIP, 2013, pp. 3–6.","mla":"Jaeger, Heinrich, et al. “From Nanoscale Cohesion to Macroscale Entanglement: Opportunities for Designing Granular Aggregate Behaviour by Tailoring Grain Shape and Interactions.” AIP Conference Proceedings, vol. 1542, AIP, 2013, pp. 3–6, doi:10.1063/1.4811858."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","conference":{"name":"Powders and Grains","start_date":"2013-07-08","end_date":"2013-07-12","location":"Sydney, Australia"},"type":"conference","status":"public","_id":"117","page":"3 - 6","date_created":"2018-12-11T11:44:43Z","doi":"10.1063/1.4811858","volume":1542,"date_published":"2013-06-01T00:00:00Z","year":"2013","publication_status":"published","language":[{"iso":"eng"}],"publication":" AIP Conference Proceedings","day":"01","quality_controlled":"1","publisher":"AIP","intvolume":" 1542","month":"06","abstract":[{"lang":"eng","text":"The packing arrangement of individual particles inside a granular material and the resulting response to applied stresses depend critically on particle-particle interactions. One aspect that recently received attention are nanoscale surface features of particles, which play an important role in determining the strength of cohesive van der Waals and capillary interactions and also affect tribo-charging of grains. We describe experiments on freely falling granular streams that can detect the contributions from all three of these forces. We show that it is possible to measure the charge of individual grains and build up distributions that are detailed enough to provide stringent tests of tribo-charging models currently available. A second aspect concerns particle shape. In this case steric interactions become important and new types of aggregate behavior can be expected when non-convex particle shapes are considered that can interlock or entangle. However, a general connection between the mechanical response of a granular material and the constituents\\' shape remains unknown. This has made it infeasible to tackle the "inverse packing problem", namely to start from a given, desired behavior for the aggregate as a whole and then find the particle shape the produces it. We discuss a new approach, using concepts rooted in artificial evolution that provides a way to solve this inverse problem. This approach facilitates exploring the role of arbitrary particle geometry in jammed systems and invites the discovery and design of granular matter with optimized properties."}],"acknowledgement":"This work was supported by the NSF MRSEC program under DMR-0820054. Additional support came from the US Army Research Office through W911NF-12-1-0182.","oa_version":"None"},{"title":"Sponsored search, market equilibria, and the Hungarian Method","author":[{"full_name":"Dütting, Paul","last_name":"Dütting","first_name":"Paul"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Weber, Ingmar","last_name":"Weber","first_name":"Ingmar"}],"external_id":{"arxiv":["0912.1934"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Dütting P, Henzinger MH, Weber I. 2013. Sponsored search, market equilibria, and the Hungarian Method. Information Processing Letters. 113(3), 67–73.","chicago":"Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Sponsored Search, Market Equilibria, and the Hungarian Method.” Information Processing Letters. Elsevier, 2013. https://doi.org/10.1016/j.ipl.2012.11.006.","ama":"Dütting P, Henzinger MH, Weber I. Sponsored search, market equilibria, and the Hungarian Method. Information Processing Letters. 2013;113(3):67-73. doi:10.1016/j.ipl.2012.11.006","apa":"Dütting, P., Henzinger, M. H., & Weber, I. (2013). Sponsored search, market equilibria, and the Hungarian Method. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2012.11.006","ieee":"P. Dütting, M. H. Henzinger, and I. Weber, “Sponsored search, market equilibria, and the Hungarian Method,” Information Processing Letters, vol. 113, no. 3. Elsevier, pp. 67–73, 2013.","short":"P. Dütting, M.H. Henzinger, I. Weber, Information Processing Letters 113 (2013) 67–73.","mla":"Dütting, Paul, et al. “Sponsored Search, Market Equilibria, and the Hungarian Method.” Information Processing Letters, vol. 113, no. 3, Elsevier, 2013, pp. 67–73, doi:10.1016/j.ipl.2012.11.006."},"quality_controlled":"1","publisher":"Elsevier","oa":1,"date_published":"2013-02-15T00:00:00Z","doi":"10.1016/j.ipl.2012.11.006","date_created":"2022-08-08T11:29:08Z","page":"67-73","day":"15","publication":"Information Processing Letters","year":"2013","status":"public","type":"journal_article","article_type":"original","_id":"11759","extern":"1","date_updated":"2022-09-12T09:36:15Z","month":"02","intvolume":" 113","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/0912.1934","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Matching markets play a prominent role in economic theory. A prime example of such a market is the sponsored search market. Here, as in other markets of that kind, market equilibria correspond to feasible, envy free, and bidder optimal outcomes. For settings without budgets such an outcome always exists and can be computed in polynomial-time by the so-called Hungarian Method. Moreover, every mechanism that computes such an outcome is incentive compatible. We show that the Hungarian Method can be modified so that it finds a feasible, envy free, and bidder optimal outcome for settings with budgets. We also show that in settings with budgets no mechanism that computes such an outcome can be incentive compatible for all inputs. For inputs in general position, however, the presented mechanism—as any other mechanism that computes such an outcome for settings with budgets—is incentive compatible."}],"volume":113,"issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0020-0190"]},"publication_status":"published"},{"publication":"40th International Colloquium on Automata, Languages, and Programming","day":"01","year":"2013","date_created":"2022-08-11T11:25:13Z","date_published":"2013-07-01T00:00:00Z","doi":"10.1007/978-3-642-39212-2_53","page":"607–619","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks,” in 40th International Colloquium on Automata, Languages, and Programming, Riga, Latvia, 2013, vol. 7966, pp. 607–619.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 40th International Colloquium on Automata, Languages, and Programming, Springer Nature, 2013, pp. 607–619.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2013). Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks. In 40th International Colloquium on Automata, Languages, and Programming (Vol. 7966, pp. 607–619). Riga, Latvia: Springer Nature. https://doi.org/10.1007/978-3-642-39212-2_53","ama":"Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks. In: 40th International Colloquium on Automata, Languages, and Programming. Vol 7966. Springer Nature; 2013:607–619. doi:10.1007/978-3-642-39212-2_53","mla":"Henzinger, Monika H., et al. “Sublinear-Time Maintenance of Breadth-First Spanning Tree in Partially Dynamic Networks.” 40th International Colloquium on Automata, Languages, and Programming, vol. 7966, Springer Nature, 2013, pp. 607–619, doi:10.1007/978-3-642-39212-2_53.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2013. Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks. 40th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 7966, 607–619.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Maintenance of Breadth-First Spanning Tree in Partially Dynamic Networks.” In 40th International Colloquium on Automata, Languages, and Programming, 7966:607–619. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-39212-2_53."},"title":"Sublinear-time maintenance of breadth-first spanning tree in partially dynamic networks","external_id":{"arxiv":["1512.08147"]},"article_processing_charge":"No","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"full_name":"Krinninger, Sebastian","last_name":"Krinninger","first_name":"Sebastian"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1611-3349"],"isbn":["9783642392115"]},"related_material":{"record":[{"relation":"later_version","status":"public","id":"11793"}]},"volume":7966,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study the problem of maintaining a breadth-first spanning tree (BFS tree) in partially dynamic distributed networks modeling a sequence of either failures or additions of communication links (but not both). We show (1 + ε)-approximation algorithms whose amortized time (over some number of link changes) is sublinear in D, the maximum diameter of the network. This breaks the Θ(D) time bound of recomputing “from scratch”.\r\n\r\nOur technique also leads to a (1 + ε)-approximate incremental algorithm for single-source shortest paths (SSSP) in the sequential (usual RAM) model. Prior to our work, the state of the art was the classic exact algorithm of [9] that is optimal under some assumptions [27]. Our result is the first to show that, in the incremental setting, this bound can be beaten in certain cases if a small approximation is allowed."}],"intvolume":" 7966","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1512.08147"}],"scopus_import":"1","alternative_title":["LNCS"],"extern":"1","date_updated":"2023-02-21T16:28:26Z","_id":"11793","status":"public","conference":{"location":"Riga, Latvia","end_date":"2013-07-12","start_date":"2013-07-08","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"type":"conference"},{"_id":"11791","status":"public","conference":{"name":"WINE: International Conference on Web and Internet Economics","start_date":"2013-12-01","end_date":"2013-12-14","location":"Cambridge, MA, USA"},"type":"conference","extern":"1","date_updated":"2023-02-13T11:20:42Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The focus of classic mechanism design has been on truthful direct-revelation mechanisms. In the context of combinatorial auctions the truthful direct-revelation mechanism that maximizes social welfare is the VCG mechanism. For many valuation spaces computing the allocation and payments of the VCG mechanism, however, is a computationally hard problem. We thus study the performance of the VCG mechanism when bidders are forced to choose bids from a subspace of the valuation space for which the VCG outcome can be computed efficiently. We prove improved upper bounds on the welfare loss for restrictions to additive bids and upper and lower bounds for restrictions to non-additive bids. These bounds show that the welfare loss increases in expressiveness. All our bounds apply to equilibrium concepts that can be computed in polynomial time as well as to learning outcomes."}],"intvolume":" 8289","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.3153"}],"scopus_import":"1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783642450457"],"issn":["1611-3349"]},"volume":8289,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.” 9th International Conference on Web and Internet Economics, vol. 8289, Springer Nature, 2013, pp. 146–159, doi:10.1007/978-3-642-45046-4_13.","ama":"Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based combinatorial auctions. In: 9th International Conference on Web and Internet Economics. Vol 8289. Springer Nature; 2013:146–159. doi:10.1007/978-3-642-45046-4_13","apa":"Dütting, P., Henzinger, M. H., & Starnberger, M. (2013). Valuation compressions in VCG-based combinatorial auctions. In 9th International Conference on Web and Internet Economics (Vol. 8289, pp. 146–159). Cambridge, MA, USA: Springer Nature. https://doi.org/10.1007/978-3-642-45046-4_13","short":"P. Dütting, M.H. Henzinger, M. Starnberger, in:, 9th International Conference on Web and Internet Economics, Springer Nature, 2013, pp. 146–159.","ieee":"P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in VCG-based combinatorial auctions,” in 9th International Conference on Web and Internet Economics, Cambridge, MA, USA, 2013, vol. 8289, pp. 146–159.","chicago":"Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions in VCG-Based Combinatorial Auctions.” In 9th International Conference on Web and Internet Economics, 8289:146–159. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-45046-4_13.","ista":"Dütting P, Henzinger MH, Starnberger M. 2013. Valuation compressions in VCG-based combinatorial auctions. 9th International Conference on Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 8289, 146–159."},"title":"Valuation compressions in VCG-based combinatorial auctions","external_id":{"arxiv":["1310.3153"]},"article_processing_charge":"No","author":[{"first_name":"Paul","full_name":"Dütting, Paul","last_name":"Dütting"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"last_name":"Starnberger","full_name":"Starnberger, Martin","first_name":"Martin"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"9th International Conference on Web and Internet Economics","day":"01","year":"2013","date_created":"2022-08-11T11:05:14Z","doi":"10.1007/978-3-642-45046-4_13","date_published":"2013-12-01T00:00:00Z","page":"146–159"},{"article_processing_charge":"No","external_id":{"arxiv":["1611.05753"]},"author":[{"first_name":"Wolfgang","last_name":"Dvořák","full_name":"Dvořák, Wolfgang"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"full_name":"Williamson, David P.","last_name":"Williamson","first_name":"David P."}],"title":"Maximizing a submodular function with viability constraints","citation":{"mla":"Dvořák, Wolfgang, et al. “Maximizing a Submodular Function with Viability Constraints.” 21st Annual European Symposium on Algorithms, vol. 8125, Springer Nature, 2013, pp. 409–20, doi:10.1007/978-3-642-40450-4_35.","ama":"Dvořák W, Henzinger MH, Williamson DP. Maximizing a submodular function with viability constraints. In: 21st Annual European Symposium on Algorithms. Vol 8125. Springer Nature; 2013:409-420. doi:10.1007/978-3-642-40450-4_35","apa":"Dvořák, W., Henzinger, M. H., & Williamson, D. P. (2013). Maximizing a submodular function with viability constraints. In 21st Annual European Symposium on Algorithms (Vol. 8125, pp. 409–420). Sophia Antipolis, France: Springer Nature. https://doi.org/10.1007/978-3-642-40450-4_35","ieee":"W. Dvořák, M. H. Henzinger, and D. P. Williamson, “Maximizing a submodular function with viability constraints,” in 21st Annual European Symposium on Algorithms, Sophia Antipolis, France, 2013, vol. 8125, pp. 409–420.","short":"W. Dvořák, M.H. Henzinger, D.P. Williamson, in:, 21st Annual European Symposium on Algorithms, Springer Nature, 2013, pp. 409–420.","chicago":"Dvořák, Wolfgang, Monika H Henzinger, and David P. Williamson. “Maximizing a Submodular Function with Viability Constraints.” In 21st Annual European Symposium on Algorithms, 8125:409–20. Springer Nature, 2013. https://doi.org/10.1007/978-3-642-40450-4_35.","ista":"Dvořák W, Henzinger MH, Williamson DP. 2013. Maximizing a submodular function with viability constraints. 21st Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LNCS, vol. 8125, 409–420."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"409 - 420","date_created":"2022-08-11T11:18:19Z","date_published":"2013-09-01T00:00:00Z","doi":"10.1007/978-3-642-40450-4_35","year":"2013","publication":"21st Annual European Symposium on Algorithms","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_updated":"2023-02-21T16:28:24Z","extern":"1","conference":{"name":"ESA: European Symposium on Algorithms","location":"Sophia Antipolis, France","end_date":"2013-09-04","start_date":"2013-09-02"},"type":"conference","status":"public","_id":"11792","related_material":{"record":[{"status":"public","id":"11792","relation":"later_version"}]},"volume":8125,"publication_status":"published","publication_identifier":{"issn":["1611-3349"],"isbn":["9783642404498"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.05753"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 8125","month":"09","abstract":[{"lang":"eng","text":"We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the so-called food web, encoding viability constraints between these species. These food webs usually have constant depth. The goal is to select a subset of k species that satisfies the viability constraints and has maximal phylogenetic diversity. As this problem is known to be NP-hard, we investigate approximation algorithm. We present the first constant factor approximation algorithm if the depth is constant. Its approximation ratio is (1−1𝑒√). This algorithm not only applies to phylogenetic trees with viability constraints but for arbitrary monotone submodular set functions with viability constraints. Second, we show that there is no (1 − 1/e + ε)-approximation algorithm for our problem setting (even for additive functions) and that there is no approximation algorithm for a slight extension of this setting."}],"oa_version":"Preprint"},{"publication_status":"published","year":"2013","publication_identifier":{"eisbn":["978-0-7695-5135-7"],"issn":["0272-5428"]},"publication":"54th Annual Symposium on Foundations of Computer Science","language":[{"iso":"eng"}],"day":"01","page":"538-547","date_created":"2022-08-16T08:22:37Z","doi":"10.1109/focs.2013.64","date_published":"2013-10-01T00:00:00Z","abstract":[{"text":"We study dynamic (1 + ϵ)-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected n-node m-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with a total update time of Ȏ(mn) and constant query time by Roditty and Zwick (FOCS 2004). The fastest deterministic algorithm is from a 1981 paper by Even and Shiloach (JACM 1981); it has a total update time of O(mn 2 ) and constant query time. We improve these results as follows: (1) We present an algorithm with a total update time of Ȏ(n 5/2 ) and constant query time that has an additive error of two in addition to the 1 + ϵ multiplicative error. This beats the previous Ȏ(mn) time when m = Ω(n 3/2 ). Note that the additive error is unavoidable since, even in the static case, an O(n 3-δ )-time (a so-called truly sub cubic) combinatorial algorithm with 1 + ϵ multiplicative error cannot have an additive error less than 2 - ϵ, unless we make a major breakthrough for Boolean matrix multiplication (Dor, Halperin and Zwick FOCS 1996) and many other long-standing problems (Vassilevska Williams and Williams FOCS 2010). The algorithm can also be turned into a (2 + ϵ)-approximation algorithm (without an additive error) with the same time guarantees, improving the recent (3 + ϵ)-approximation algorithm with Ȏ(n 5/2+O(1√(log n)) ) running time of Bernstein and Roditty (SODA 2011) in terms of both approximation and time guarantees. (2) We present a deterministic algorithm with a total update time of Ȏ(mn) and a query time of O(log log n). The algorithm has a multiplicative error of 1 + ϵ and gives the first improved deterministic algorithm since 1981. It also answers an open question raised by Bernstein in his STOC 2013 paper. In order to achieve our results, we introduce two new techniques: (1) A lazy Even-Shiloach tree algorithm which maintains a bounded-distance shortest-paths tree on a certain type of emulator called locally persevering emulator. (2) A derandomization technique based on moving Even-Shiloach trees as a way to derandomize the standard random set argument. These techniques might be of independent interest.","lang":"eng"}],"oa_version":"Preprint","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1308.0776","open_access":"1"}],"scopus_import":"1","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","month":"10","citation":{"mla":"Henzinger, Monika H., et al. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” 54th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2013, pp. 538–47, doi:10.1109/focs.2013.64.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. In: 54th Annual Symposium on Foundations of Computer Science. Institute of Electrical and Electronics Engineers; 2013:538-547. doi:10.1109/focs.2013.64","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2013). Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. In 54th Annual Symposium on Foundations of Computer Science (pp. 538–547). Berkeley, CA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2013.64","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization,” in 54th Annual Symposium on Foundations of Computer Science, Berkeley, CA, United States, 2013, pp. 538–547.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 54th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2013, pp. 538–547.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Dynamic Approximate All-Pairs Shortest Paths: Breaking the O(Mn) Barrier and Derandomization.” In 54th Annual Symposium on Foundations of Computer Science, 538–47. Institute of Electrical and Electronics Engineers, 2013. https://doi.org/10.1109/focs.2013.64.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2013. Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization. 54th Annual Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science, 538–547."},"date_updated":"2023-02-17T09:56:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","external_id":{"arxiv":["1308.0776"]},"author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"full_name":"Nanongkai, Danupon","last_name":"Nanongkai","first_name":"Danupon"}],"title":"Dynamic approximate all-pairs shortest paths: Breaking the O(mn) barrier and derandomization","_id":"11856","conference":{"name":"FOCS: Symposium on Foundations of Computer Science","start_date":"2013-10-26","location":"Berkeley, CA, United States","end_date":"2013-10-29"},"type":"conference","status":"public"},{"_id":"11902","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-21T16:28:41Z","extern":"1","abstract":[{"lang":"eng","text":"We study the problem of matching bidders to items where each bidder i has general, strictly monotonic utility functions ui,j(pj) expressing his utility of being matched to item j at price pj. For this setting we prove that a bidder optimal outcome always exists, even when the utility functions are non-linear and non-continuous. We give sufficient conditions under\r\nwhich every mechanism that finds a bidder optimal outcome is incentive compatible. We also give a mechanism that finds a bidder optimal outcome if the conditions for incentive compatibility are satisfied. The running time of this mechanism is exponential in the number of items, but polynomial in the number of bidders."}],"oa_version":"None","scopus_import":"1","month":"03","intvolume":" 478","publication_identifier":{"issn":["0304-3975"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"11799"}]},"issue":"3","volume":478,"citation":{"ama":"Dütting P, Henzinger MH, Weber I. Bidder optimal assignments for general utilities. Theoretical Computer Science. 2013;478(3):22-32. doi:10.1016/j.tcs.2013.01.030","apa":"Dütting, P., Henzinger, M. H., & Weber, I. (2013). Bidder optimal assignments for general utilities. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2013.01.030","short":"P. Dütting, M.H. Henzinger, I. Weber, Theoretical Computer Science 478 (2013) 22–32.","ieee":"P. Dütting, M. H. Henzinger, and I. Weber, “Bidder optimal assignments for general utilities,” Theoretical Computer Science, vol. 478, no. 3. Elsevier, pp. 22–32, 2013.","mla":"Dütting, Paul, et al. “Bidder Optimal Assignments for General Utilities.” Theoretical Computer Science, vol. 478, no. 3, Elsevier, 2013, pp. 22–32, doi:10.1016/j.tcs.2013.01.030.","ista":"Dütting P, Henzinger MH, Weber I. 2013. Bidder optimal assignments for general utilities. Theoretical Computer Science. 478(3), 22–32.","chicago":"Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Bidder Optimal Assignments for General Utilities.” Theoretical Computer Science. Elsevier, 2013. https://doi.org/10.1016/j.tcs.2013.01.030."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Paul","full_name":"Dütting, Paul","last_name":"Dütting"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Weber","full_name":"Weber, Ingmar","first_name":"Ingmar"}],"article_processing_charge":"No","title":"Bidder optimal assignments for general utilities","quality_controlled":"1","publisher":"Elsevier","year":"2013","day":"25","publication":"Theoretical Computer Science","page":"22-32","date_published":"2013-03-25T00:00:00Z","doi":"10.1016/j.tcs.2013.01.030","date_created":"2022-08-17T11:11:04Z"},{"type":"journal_article","article_type":"letter_note","status":"public","_id":"11959","article_processing_charge":"No","author":[{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"full_name":"Martinez, Sabrina Teixeira","last_name":"Martinez","first_name":"Sabrina Teixeira"},{"first_name":"David","full_name":"Cantillo, David","last_name":"Cantillo"},{"first_name":"C. Oliver","last_name":"Kappe","full_name":"Kappe, C. Oliver"}],"title":"In situ generation of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins","citation":{"ista":"Pieber B, Martinez ST, Cantillo D, Kappe CO. 2013. In situ generation of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins. Angewandte Chemie International Edition. 52(39), 10241–10244.","chicago":"Pieber, Bartholomäus, Sabrina Teixeira Martinez, David Cantillo, and C. Oliver Kappe. “In Situ Generation of Diimide from Hydrazine and Oxygen: Continuous-Flow Transfer Hydrogenation of Olefins.” Angewandte Chemie International Edition. Wiley, 2013. https://doi.org/10.1002/anie.201303528.","ieee":"B. Pieber, S. T. Martinez, D. Cantillo, and C. O. Kappe, “In situ generation of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins,” Angewandte Chemie International Edition, vol. 52, no. 39. Wiley, pp. 10241–10244, 2013.","short":"B. Pieber, S.T. Martinez, D. Cantillo, C.O. Kappe, Angewandte Chemie International Edition 52 (2013) 10241–10244.","apa":"Pieber, B., Martinez, S. T., Cantillo, D., & Kappe, C. O. (2013). In situ generation of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201303528","ama":"Pieber B, Martinez ST, Cantillo D, Kappe CO. In situ generation of diimide from hydrazine and oxygen: Continuous-flow transfer hydrogenation of olefins. Angewandte Chemie International Edition. 2013;52(39):10241-10244. doi:10.1002/anie.201303528","mla":"Pieber, Bartholomäus, et al. “In Situ Generation of Diimide from Hydrazine and Oxygen: Continuous-Flow Transfer Hydrogenation of Olefins.” Angewandte Chemie International Edition, vol. 52, no. 39, Wiley, 2013, pp. 10241–44, doi:10.1002/anie.201303528."},"date_updated":"2023-02-21T10:09:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","scopus_import":"1","quality_controlled":"1","publisher":"Wiley","intvolume":" 52","month":"09","abstract":[{"lang":"eng","text":"No catalyst required! A highly efficient, catalyst-free process to generate diimide in situ from hydrazine monohydrate and molecular oxygen for the selective reduction of alkenes has been developed. The use of a gas–liquid segmented flow system allowed safe operating conditions and dramatically enhanced this atom-economical reaction, resulting in short processing times."}],"oa_version":"None","page":"10241-10244","date_created":"2022-08-24T11:01:47Z","volume":52,"issue":"39","date_published":"2013-09-23T00:00:00Z","doi":"10.1002/anie.201303528","year":"2013","publication_status":"published","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publication":"Angewandte Chemie International Edition","language":[{"iso":"eng"}],"day":"23"},{"status":"public","type":"journal_article","article_type":"letter_note","_id":"11960","title":"Microwave effects in organic synthesis: Myth or reality?","article_processing_charge":"No","author":[{"first_name":"C. Oliver","last_name":"Kappe","full_name":"Kappe, C. Oliver"},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"first_name":"Doris","last_name":"Dallinger","full_name":"Dallinger, Doris"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2023-02-21T10:09:26Z","citation":{"ista":"Kappe CO, Pieber B, Dallinger D. 2013. Microwave effects in organic synthesis: Myth or reality? Angewandte Chemie International Edition. 52(4), 1088–1094.","chicago":"Kappe, C. Oliver, Bartholomäus Pieber, and Doris Dallinger. “Microwave Effects in Organic Synthesis: Myth or Reality?” Angewandte Chemie International Edition. Wiley, 2013. https://doi.org/10.1002/anie.201204103.","apa":"Kappe, C. O., Pieber, B., & Dallinger, D. (2013). Microwave effects in organic synthesis: Myth or reality? Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201204103","ama":"Kappe CO, Pieber B, Dallinger D. Microwave effects in organic synthesis: Myth or reality? Angewandte Chemie International Edition. 2013;52(4):1088-1094. doi:10.1002/anie.201204103","ieee":"C. O. Kappe, B. Pieber, and D. Dallinger, “Microwave effects in organic synthesis: Myth or reality?,” Angewandte Chemie International Edition, vol. 52, no. 4. Wiley, pp. 1088–1094, 2013.","short":"C.O. Kappe, B. Pieber, D. Dallinger, Angewandte Chemie International Edition 52 (2013) 1088–1094.","mla":"Kappe, C. Oliver, et al. “Microwave Effects in Organic Synthesis: Myth or Reality?” Angewandte Chemie International Edition, vol. 52, no. 4, Wiley, 2013, pp. 1088–94, doi:10.1002/anie.201204103."},"intvolume":" 52","month":"01","scopus_import":"1","publisher":"Wiley","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"It's not magic! The effects observed in microwave-irradiated chemical transformations can in most cases be rationalized by purely bulk thermal phenomena associated with rapid heating to elevated temperatures. As discussed in this Essay, the existence of so-called nonthermal or specific microwave effects is highly doubtful."}],"date_created":"2022-08-24T11:05:04Z","issue":"4","doi":"10.1002/anie.201204103","date_published":"2013-01-21T00:00:00Z","volume":52,"page":"1088-1094","publication":"Angewandte Chemie International Edition","language":[{"iso":"eng"}],"day":"21","year":"2013","publication_status":"published","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]}},{"article_processing_charge":"No","author":[{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus","last_name":"Pieber"},{"last_name":"Kappe","full_name":"Kappe, C. Oliver","first_name":"C. Oliver"}],"title":"Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid continuous-flow regime using propylene carbonate as a solvent","date_updated":"2023-02-21T10:09:54Z","citation":{"apa":"Pieber, B., & Kappe, C. O. (2013). Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid continuous-flow regime using propylene carbonate as a solvent. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36896j","ama":"Pieber B, Kappe CO. Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid continuous-flow regime using propylene carbonate as a solvent. Green Chemistry. 2013;15(2):320-324. doi:10.1039/c2gc36896j","short":"B. Pieber, C.O. Kappe, Green Chemistry 15 (2013) 320–324.","ieee":"B. Pieber and C. O. Kappe, “Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid continuous-flow regime using propylene carbonate as a solvent,” Green Chemistry, vol. 15, no. 2. Royal Society of Chemistry, pp. 320–324, 2013.","mla":"Pieber, Bartholomäus, and C. Oliver Kappe. “Direct Aerobic Oxidation of 2-Benzylpyridines in a Gas-Liquid Continuous-Flow Regime Using Propylene Carbonate as a Solvent.” Green Chemistry, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 320–24, doi:10.1039/c2gc36896j.","ista":"Pieber B, Kappe CO. 2013. Direct aerobic oxidation of 2-benzylpyridines in a gas-liquid continuous-flow regime using propylene carbonate as a solvent. Green Chemistry. 15(2), 320–324.","chicago":"Pieber, Bartholomäus, and C. Oliver Kappe. “Direct Aerobic Oxidation of 2-Benzylpyridines in a Gas-Liquid Continuous-Flow Regime Using Propylene Carbonate as a Solvent.” Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36896j."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","article_type":"letter_note","status":"public","_id":"11973","page":"320-324","date_created":"2022-08-25T10:29:21Z","doi":"10.1039/c2gc36896j","issue":"2","date_published":"2013-02-01T00:00:00Z","volume":15,"publication_status":"published","year":"2013","publication_identifier":{"eissn":["1463-9270"],"issn":["1463-9262"]},"language":[{"iso":"eng"}],"publication":"Green Chemistry","day":"01","scopus_import":"1","publisher":"Royal Society of Chemistry","quality_controlled":"1","intvolume":" 15","month":"02","abstract":[{"text":"The use of high-temperature/pressure gas–liquid continuous flow conditions dramatically enhances the iron-catalyzed aerobic oxidation of 2-benzylpyridines to their corresponding ketones. Pressurized air serves as a readily available oxygen source and propylene carbonate as a green solvent in this radically intensified preparation of synthetically valuable 2-aroylpyridines.","lang":"eng"}],"oa_version":"None"},{"author":[{"full_name":"Petersen, Lene","last_name":"Petersen","first_name":"Lene"},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"},{"first_name":"Inge","last_name":"Juszak","full_name":"Juszak, Inge"},{"first_name":"Marco","last_name":"Carenzo","full_name":"Carenzo, Marco"},{"full_name":"Brock, Ben","last_name":"Brock","first_name":"Ben"}],"article_processing_charge":"No","title":"Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative","citation":{"ista":"Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. 2013. Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. Annals of Glaciology. 54(63), 120–130.","chicago":"Petersen, Lene, Francesca Pellicciotti, Inge Juszak, Marco Carenzo, and Ben Brock. “Suitability of a Constant Air Temperature Lapse Rate over an Alpine Glacier: Testing the Greuell and Böhm Model as an Alternative.” Annals of Glaciology. International Glaciological Society, 2013. https://doi.org/10.3189/2013aog63a477.","apa":"Petersen, L., Pellicciotti, F., Juszak, I., Carenzo, M., & Brock, B. (2013). Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. Annals of Glaciology. International Glaciological Society. https://doi.org/10.3189/2013aog63a477","ama":"Petersen L, Pellicciotti F, Juszak I, Carenzo M, Brock B. Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative. Annals of Glaciology. 2013;54(63):120-130. doi:10.3189/2013aog63a477","ieee":"L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, and B. Brock, “Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative,” Annals of Glaciology, vol. 54, no. 63. International Glaciological Society, pp. 120–130, 2013.","short":"L. Petersen, F. Pellicciotti, I. Juszak, M. Carenzo, B. Brock, Annals of Glaciology 54 (2013) 120–130.","mla":"Petersen, Lene, et al. “Suitability of a Constant Air Temperature Lapse Rate over an Alpine Glacier: Testing the Greuell and Böhm Model as an Alternative.” Annals of Glaciology, vol. 54, no. 63, International Glaciological Society, 2013, pp. 120–30, doi:10.3189/2013aog63a477."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"International Glaciological Society","oa":1,"page":"120-130","doi":"10.3189/2013aog63a477","date_published":"2013-08-01T00:00:00Z","date_created":"2023-02-20T08:17:29Z","year":"2013","day":"01","publication":"Annals of Glaciology","type":"journal_article","article_type":"original","status":"public","keyword":["Earth-Surface Processes"],"_id":"12642","date_updated":"2023-02-21T10:18:24Z","extern":"1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2013aog63a477"}],"month":"08","intvolume":" 54","abstract":[{"text":"Near-surface air temperature, typically measured at a height of 2 m, is the most important control on the energy exchange and the melt rate at a snow or ice surface. It is distributed in a simplistic manner in most glacier melt models by using constant linear lapse rates, which poorly represent the actual spatial and temporal variability of air temperature. In this paper, we test a simple thermodynamic model proposed by Greuell and Böhm in 1998 as an alternative, using a new dataset of air temperature measurements from along the flowline of Haut Glacier d’Arolla, Switzerland. The unmodified model performs little better than assuming a constant linear lapse rate. When modified to allow the ratio of the boundary layer height to the bulk heat transfer coefficient to vary along the flowline, the model matches measured air temperatures better, and a further reduction of the root-mean-square error is obtained, although there is still considerable scope for improvement. The modified model is shown to perform best under conditions favourable to the development of katabatic winds – few clouds, positive ambient air temperature, limited influence of synoptic or valley winds and a long fetch – but its performance is poor under cloudy conditions.","lang":"eng"}],"oa_version":"Published Version","issue":"63","volume":54,"publication_identifier":{"eissn":["1727-5644"],"issn":["0260-3055"]},"publication_status":"published","language":[{"iso":"eng"}]},{"volume":118,"issue":"8","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2169-897X"]},"intvolume":" 118","month":"04","main_file_link":[{"url":"https://doi.org/10.1002/jgrd.50277","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Parameterizations of incoming longwave radiation are increasingly receiving attention for both low and high elevation glacierized sites. In this paper, we test 13 clear-sky parameterizations combined with seven cloud corrections for all-sky atmospheric emissivity at one location on Haut Glacier d'Arolla. We also analyze the four seasons separately and conduct a cross-validation to test the parameters’ robustness. The best parameterization is the one by Dilley and O'Brien, B for clear-sky conditions combined with Unsworth and Monteith cloud correction. This model is also the most robust when tested in cross-validation. When validated at different sites in the southern Alps of Switzerland and north-western Italian Alps, all parameterizations show a substantial decrease in performance, except for one site, thus suggesting that it is important to recalibrate parameterizations of incoming longwave radiation for different locations. We argue that this is due to differences in the structure of the atmosphere at the sites. We also quantify the effect that the incoming longwave radiation parameterizations have on energy-balance melt modeling, and show that recalibration of model parameters is needed. Using parameters from other sites leads to a significant underestimation of melt and to an error that is larger than that associated with using different parameterizations. Once recalibrated, however, the parameters of most models seem to be stable over seasons and years at the location on Haut Glacier d'Arolla."}],"extern":"1","date_updated":"2023-02-21T10:10:46Z","keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"status":"public","article_type":"original","type":"journal_article","_id":"12643","date_created":"2023-02-20T08:17:34Z","doi":"10.1002/jgrd.50277","date_published":"2013-04-27T00:00:00Z","page":"3066-3084","publication":"Journal of Geophysical Research: Atmospheres","day":"27","year":"2013","oa":1,"quality_controlled":"1","publisher":"American Geophysical Union","title":"A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability","article_processing_charge":"No","author":[{"last_name":"Juszak","full_name":"Juszak, I.","first_name":"I."},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal Variability.” Journal of Geophysical Research: Atmospheres, vol. 118, no. 8, American Geophysical Union, 2013, pp. 3066–84, doi:10.1002/jgrd.50277.","ama":"Juszak I, Pellicciotti F. A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. Journal of Geophysical Research: Atmospheres. 2013;118(8):3066-3084. doi:10.1002/jgrd.50277","apa":"Juszak, I., & Pellicciotti, F. (2013). A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/jgrd.50277","short":"I. Juszak, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 118 (2013) 3066–3084.","ieee":"I. Juszak and F. Pellicciotti, “A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability,” Journal of Geophysical Research: Atmospheres, vol. 118, no. 8. American Geophysical Union, pp. 3066–3084, 2013.","chicago":"Juszak, I., and Francesca Pellicciotti. “A Comparison of Parameterizations of Incoming Longwave Radiation over Melting Glaciers: Model Robustness and Seasonal Variability.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2013. https://doi.org/10.1002/jgrd.50277.","ista":"Juszak I, Pellicciotti F. 2013. A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability. Journal of Geophysical Research: Atmospheres. 118(8), 3066–3084."}},{"publisher":"Springer Nature","quality_controlled":"1","page":"742-745","date_created":"2023-02-20T08:17:17Z","date_published":"2013-09-13T00:00:00Z","doi":"10.1038/ngeo1896","year":"2013","publication":"Nature Geoscience","day":"13","article_processing_charge":"No","author":[{"first_name":"W. W.","full_name":"Immerzeel, W. W.","last_name":"Immerzeel"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"},{"last_name":"Bierkens","full_name":"Bierkens, M. F. P.","first_name":"M. F. P."}],"title":"Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds","citation":{"chicago":"Immerzeel, W. W., Francesca Pellicciotti, and M. F. P. Bierkens. “Rising River Flows throughout the Twenty-First Century in Two Himalayan Glacierized Watersheds.” Nature Geoscience. Springer Nature, 2013. https://doi.org/10.1038/ngeo1896.","ista":"Immerzeel WW, Pellicciotti F, Bierkens MFP. 2013. Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. Nature Geoscience. 6(9), 742–745.","mla":"Immerzeel, W. W., et al. “Rising River Flows throughout the Twenty-First Century in Two Himalayan Glacierized Watersheds.” Nature Geoscience, vol. 6, no. 9, Springer Nature, 2013, pp. 742–45, doi:10.1038/ngeo1896.","ieee":"W. W. Immerzeel, F. Pellicciotti, and M. F. P. Bierkens, “Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds,” Nature Geoscience, vol. 6, no. 9. Springer Nature, pp. 742–745, 2013.","short":"W.W. Immerzeel, F. Pellicciotti, M.F.P. Bierkens, Nature Geoscience 6 (2013) 742–745.","ama":"Immerzeel WW, Pellicciotti F, Bierkens MFP. Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. Nature Geoscience. 2013;6(9):742-745. doi:10.1038/ngeo1896","apa":"Immerzeel, W. W., Pellicciotti, F., & Bierkens, M. F. P. (2013). Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds. Nature Geoscience. Springer Nature. https://doi.org/10.1038/ngeo1896"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 6","month":"09","abstract":[{"text":"Greater Himalayan glaciers are retreating and losing mass at rates comparable to glaciers in other regions of the world1,2,3,4,5. Assessments of future changes and their associated hydrological impacts are scarce, oversimplify glacier dynamics or include a limited number of climate models6,7,8,9. Here, we use results from the latest ensemble of climate models in combination with a high-resolution glacio-hydrological model to assess the hydrological impact of climate change on two climatically contrasting watersheds in the Greater Himalaya, the Baltoro and Langtang watersheds that drain into the Indus and Ganges rivers, respectively. We show that the largest uncertainty in future runoff is a result of variations in projected precipitation between climate models. In both watersheds, strong, but highly variable, increases in future runoff are projected and, despite the different characteristics of the watersheds, their responses are surprisingly similar. In both cases, glaciers will recede but net glacier melt runoff is on a rising limb at least until 2050. In combination with a positive change in precipitation, water availability during this century is not likely to decline. We conclude that river basins that depend on monsoon rains and glacier melt will continue to sustain the increasing water demands expected in these areas10.","lang":"eng"}],"oa_version":"None","issue":"9","volume":6,"publication_status":"published","publication_identifier":{"issn":["1752-0894"],"eissn":["1752-0908"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"letter_note","keyword":["General Earth and Planetary Sciences"],"status":"public","_id":"12640","date_updated":"2023-02-21T10:46:37Z","extern":"1"},{"month":"08","intvolume":" 54","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.3189/2013aog63a537","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"We investigate the sensitivity of a distributed enhanced temperature-index (ETI) melt model, in order to understand which parameters have the largest influence on model outputs and thus need to be accurately known. We use melt and meteorological data from two Alpine glaciers and one glacier in the Andes of Chile. Sensitivity analysis is conducted in a systematic way in terms of parameters and the different conditions (day, night, clear-sky, overcast), melt seasons and glaciers examined. The sensitivity of total melt to changes in individual parameters is calculated using a local method around the optimal value of the parameters. We verify that the parameters are optimal at the distributed scale and assess the model uncertainty induced by uncertainty in the parameters using a Monte Carlo technique. Model sensitivity to parameters is consistent across melt seasons, glaciers, different conditions and the daily statistics examined. The parameters to which the model is most sensitive are the shortwave-radiation factor, the temperature lapse rate for extrapolation of air temperature, the albedo parameters, the temperature threshold and the cloud transmittance factor parameters. A parameter uncertainty of 5% results in a model uncertainty of 5.6% of mean melt on Haut Glacier d’Arolla, Switzerland.","lang":"eng"}],"issue":"63","volume":54,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0260-3055"],"eissn":["1727-5644"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"12641","extern":"1","date_updated":"2023-02-21T10:43:42Z","publisher":"International Glaciological Society","quality_controlled":"1","oa":1,"doi":"10.3189/2013aog63a537","date_published":"2013-08-01T00:00:00Z","date_created":"2023-02-20T08:17:21Z","page":"311-321","day":"01","publication":"Annals of Glaciology","year":"2013","title":"Parameter sensitivity of a distributed enhanced temperature-index melt model","author":[{"first_name":"Martin","full_name":"Heynen, Martin","last_name":"Heynen"},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"first_name":"Marco","last_name":"Carenzo","full_name":"Carenzo, Marco"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Heynen, Martin, et al. “Parameter Sensitivity of a Distributed Enhanced Temperature-Index Melt Model.” Annals of Glaciology, vol. 54, no. 63, International Glaciological Society, 2013, pp. 311–21, doi:10.3189/2013aog63a537.","ama":"Heynen M, Pellicciotti F, Carenzo M. Parameter sensitivity of a distributed enhanced temperature-index melt model. Annals of Glaciology. 2013;54(63):311-321. doi:10.3189/2013aog63a537","apa":"Heynen, M., Pellicciotti, F., & Carenzo, M. (2013). Parameter sensitivity of a distributed enhanced temperature-index melt model. Annals of Glaciology. International Glaciological Society. https://doi.org/10.3189/2013aog63a537","short":"M. Heynen, F. Pellicciotti, M. Carenzo, Annals of Glaciology 54 (2013) 311–321.","ieee":"M. Heynen, F. Pellicciotti, and M. Carenzo, “Parameter sensitivity of a distributed enhanced temperature-index melt model,” Annals of Glaciology, vol. 54, no. 63. International Glaciological Society, pp. 311–321, 2013.","chicago":"Heynen, Martin, Francesca Pellicciotti, and Marco Carenzo. “Parameter Sensitivity of a Distributed Enhanced Temperature-Index Melt Model.” Annals of Glaciology. International Glaciological Society, 2013. https://doi.org/10.3189/2013aog63a537.","ista":"Heynen M, Pellicciotti F, Carenzo M. 2013. Parameter sensitivity of a distributed enhanced temperature-index melt model. Annals of Glaciology. 54(63), 311–321."}},{"month":"01","intvolume":" 33","publisher":"Society for Neuroscience","quality_controlled":0,"acknowledgement":"This work was supported by the Max Planck Society. ","abstract":[{"text":"When confronted with a large-field stimulus rotating around the vertical body axis, flies display a following behavior called "optomotor response." As neural control elements, the large tangential horizontal system (HS) cells of the lobula plate have been prime candidates for long. Here, we applied optogenetic stimulation of HS cells to evaluate their behavioral role in Drosophila. To minimize interference of the optical activation of channelrhodopsin-2 with the visual perception of the flies, we used a bistable variant called ChR2-C128S. By applying pulses of blue and yellow light, we first demonstrate electrophysiologically that lobula plate tangential cells can be activated and deactivated repeatedly with no evident change in depolarization strength over trials. We next show that selective optogenetic activation of HS cells elicits robust yaw head movements and yaw turning responses in fixed and tethered flying flies, respectively.","lang":"eng"}],"volume":33,"issue":"34","doi":"10.1523/JNEUROSCI.0340-13.2013","date_published":"2013-01-01T00:00:00Z","date_created":"2018-12-11T11:51:16Z","page":"13927 - 13934","day":"01","publication":"Journal of Neuroscience","year":"2013","publication_status":"published","status":"public","type":"journal_article","_id":"1304","title":"Optogenetic control of fly optomotor responses","author":[{"full_name":"Haikala, Väinö","last_name":"Haikala","first_name":"Väinö"},{"last_name":"Jösch","full_name":"Maximilian Jösch","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"},{"full_name":"Borst, Alexander","last_name":"Borst","first_name":"Alexander"},{"last_name":"Mauss","full_name":"Mauss, Alex S","first_name":"Alex"}],"publist_id":"5967","extern":1,"citation":{"short":"V. Haikala, M.A. Jösch, A. Borst, A. Mauss, Journal of Neuroscience 33 (2013) 13927–13934.","ieee":"V. Haikala, M. A. Jösch, A. Borst, and A. Mauss, “Optogenetic control of fly optomotor responses,” Journal of Neuroscience, vol. 33, no. 34. Society for Neuroscience, pp. 13927–13934, 2013.","apa":"Haikala, V., Jösch, M. A., Borst, A., & Mauss, A. (2013). Optogenetic control of fly optomotor responses. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0340-13.2013","ama":"Haikala V, Jösch MA, Borst A, Mauss A. Optogenetic control of fly optomotor responses. Journal of Neuroscience. 2013;33(34):13927-13934. doi:10.1523/JNEUROSCI.0340-13.2013","mla":"Haikala, Väinö, et al. “Optogenetic Control of Fly Optomotor Responses.” Journal of Neuroscience, vol. 33, no. 34, Society for Neuroscience, 2013, pp. 13927–34, doi:10.1523/JNEUROSCI.0340-13.2013.","ista":"Haikala V, Jösch MA, Borst A, Mauss A. 2013. Optogenetic control of fly optomotor responses. Journal of Neuroscience. 33(34), 13927–13934.","chicago":"Haikala, Väinö, Maximilian A Jösch, Alexander Borst, and Alex Mauss. “Optogenetic Control of Fly Optomotor Responses.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.0340-13.2013."},"date_updated":"2021-01-12T06:49:45Z"},{"publist_id":"5968","author":[{"last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Maximilian Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Franz","last_name":"Weber","full_name":"Weber, Franz"},{"last_name":"Eichner","full_name":"Eichner, Hubert","first_name":"Hubert"},{"first_name":"Alexander","last_name":"Borst","full_name":"Borst, Alexander"}],"title":"Functional specialization of parallel motion detection circuits in the fly","citation":{"mla":"Jösch, Maximilian A., et al. “Functional Specialization of Parallel Motion Detection Circuits in the Fly.” Journal of Neuroscience, vol. 33, no. 3, Society for Neuroscience, 2013, pp. 902–05, doi:10.1523/JNEUROSCI.3374-12.2013.","ama":"Jösch MA, Weber F, Eichner H, Borst A. Functional specialization of parallel motion detection circuits in the fly. Journal of Neuroscience. 2013;33(3):902-905. doi:10.1523/JNEUROSCI.3374-12.2013","apa":"Jösch, M. A., Weber, F., Eichner, H., & Borst, A. (2013). Functional specialization of parallel motion detection circuits in the fly. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.3374-12.2013","ieee":"M. A. Jösch, F. Weber, H. Eichner, and A. Borst, “Functional specialization of parallel motion detection circuits in the fly,” Journal of Neuroscience, vol. 33, no. 3. Society for Neuroscience, pp. 902–905, 2013.","short":"M.A. Jösch, F. Weber, H. Eichner, A. Borst, Journal of Neuroscience 33 (2013) 902–905.","chicago":"Jösch, Maximilian A, Franz Weber, Hubert Eichner, and Alexander Borst. “Functional Specialization of Parallel Motion Detection Circuits in the Fly.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.3374-12.2013.","ista":"Jösch MA, Weber F, Eichner H, Borst A. 2013. Functional specialization of parallel motion detection circuits in the fly. Journal of Neuroscience. 33(3), 902–905."},"date_updated":"2021-01-12T06:49:45Z","extern":1,"type":"journal_article","status":"public","_id":"1305","page":"902 - 905","issue":"3","date_published":"2013-01-16T00:00:00Z","doi":"10.1523/JNEUROSCI.3374-12.2013","volume":33,"date_created":"2018-12-11T11:51:16Z","publication_status":"published","year":"2013","day":"16","publication":"Journal of Neuroscience","quality_controlled":0,"publisher":"Society for Neuroscience","month":"01","intvolume":" 33","abstract":[{"lang":"eng","text":"In the fly Drosophila melanogaster, photoreceptor input to motion vision is split into two parallel pathways as represented by first-order interneurons L1 and L2 (Rister et al., 2007; Joesch et al., 2010). However, how these pathways are functionally specialized remains controversial. One study (Eichner et al., 2011) proposed that the L1-pathway evaluates only sequences of brightness increments (ON-ON), while the L2-pathway processes exclusively brightness decrements (OFF-OFF). Another study (Clark et al., 2011) proposed that each of the two pathways evaluates both ON-ON and OFF-OFF sequences. To decide between these alternatives, we recorded from motionsensitive neurons in flies in which the output from either L1 or L2 was genetically blocked. We found that blocking L1 abolishes ON-ON responses but leaves OFF-OFF responses intact. The opposite was true, when the output from L2 was blocked. We conclude that the L1 and L2 pathways are functionally specialized to detect ON-ON and OFF-OFF sequences, respectively."}],"acknowledgement":"This work was supported by the Max-Planck-Society and the SFB 870 of the Deutsche Forschungsgemeinschaft."},{"date_created":"2018-12-11T11:51:17Z","date_published":"2013-01-01T00:00:00Z","issue":"3","doi":"10.1137/120874291","volume":45,"page":"1585 - 1615","publication":"SIAM Journal on Mathematical Analysis","day":"01","publication_status":"published","year":"2013","intvolume":" 45","month":"01","publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":0,"abstract":[{"lang":"eng","text":"We derive sufficient conditions for advection-driven backward motion of the free boundary in a chemotaxis model with degenerate mobility. In this model, a porous-medium-type diffusive term and an advection term are in competition. The former induces forward motion, the latter may induce backward motion of the free boundary depending on the direction of advection. We deduce conditions on the growth of the initial data at the free boundary which ensure that at least initially the advection term is dominant. This implies local backward motion of the free boundary provided the advection is (locally) directed appropriately. Our result is based on a new class of moving test functions and Stampacchia's lemma. As a by-product of our estimates, we obtain quantitative bounds on the spreading of the support of solutions for the chemotaxis model and provide a proof for the finite speed of the support propagation property of solutions."}],"title":"Advection-driven support shrinking in a chemotaxis model with degenerate mobility","author":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Julian Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5963","extern":1,"date_updated":"2021-01-12T06:49:46Z","citation":{"mla":"Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis Model with Degenerate Mobility.” SIAM Journal on Mathematical Analysis, vol. 45, no. 3, Society for Industrial and Applied Mathematics , 2013, pp. 1585–615, doi:10.1137/120874291.","ama":"Fischer JL. Advection-driven support shrinking in a chemotaxis model with degenerate mobility. SIAM Journal on Mathematical Analysis. 2013;45(3):1585-1615. doi:10.1137/120874291","apa":"Fischer, J. L. (2013). Advection-driven support shrinking in a chemotaxis model with degenerate mobility. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/120874291","ieee":"J. L. Fischer, “Advection-driven support shrinking in a chemotaxis model with degenerate mobility,” SIAM Journal on Mathematical Analysis, vol. 45, no. 3. Society for Industrial and Applied Mathematics , pp. 1585–1615, 2013.","short":"J.L. Fischer, SIAM Journal on Mathematical Analysis 45 (2013) 1585–1615.","chicago":"Fischer, Julian L. “Advection-Driven Support Shrinking in a Chemotaxis Model with Degenerate Mobility.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120874291.","ista":"Fischer JL. 2013. Advection-driven support shrinking in a chemotaxis model with degenerate mobility. SIAM Journal on Mathematical Analysis. 45(3), 1585–1615."},"status":"public","type":"journal_article","_id":"1308"},{"type":"journal_article","status":"public","_id":"1307","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","full_name":"Julian Fischer","orcid":"0000-0002-0479-558X"}],"publist_id":"5962","title":"Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models","date_updated":"2021-01-12T06:49:46Z","citation":{"ista":"Fischer JL. 2013. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. Communications in Partial Differential Equations. 38(11), 2004–2047.","chicago":"Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift Diffusion Models.” Communications in Partial Differential Equations. Taylor & Francis, 2013. https://doi.org/10.1080/03605302.2013.823548.","apa":"Fischer, J. L. (2013). Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. Communications in Partial Differential Equations. Taylor & Francis. https://doi.org/10.1080/03605302.2013.823548","ama":"Fischer JL. Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models. Communications in Partial Differential Equations. 2013;38(11):2004-2047. doi:10.1080/03605302.2013.823548","short":"J.L. Fischer, Communications in Partial Differential Equations 38 (2013) 2004–2047.","ieee":"J. L. Fischer, “Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models,” Communications in Partial Differential Equations, vol. 38, no. 11. Taylor & Francis, pp. 2004–2047, 2013.","mla":"Fischer, Julian L. “Uniqueness of Solutions of the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift Diffusion Models.” Communications in Partial Differential Equations, vol. 38, no. 11, Taylor & Francis, 2013, pp. 2004–47, doi:10.1080/03605302.2013.823548."},"extern":1,"publisher":"Taylor & Francis","quality_controlled":0,"intvolume":" 38","month":"11","abstract":[{"lang":"eng","text":"We prove uniqueness of solutions of the DLSS equation in a class of sufficiently regular functions. The global weak solutions of the DLSS equation constructed by Jüngel and Matthes belong to this class of uniqueness. We also show uniqueness of solutions for the quantum drift-diffusion equation, which contains additional drift and second-order diffusion terms. The results hold in case of periodic or Dirichlet-Neumann boundary conditions. Our proof is based on a monotonicity property of the DLSS operator and sophisticated approximation arguments; we derive a PDE satisfied by the pointwise square root of the solution, which enables us to exploit the monotonicity property of the operator."}],"page":"2004 - 2047","date_created":"2018-12-11T11:51:17Z","date_published":"2013-11-01T00:00:00Z","volume":38,"doi":"10.1080/03605302.2013.823548","issue":"11","year":"2013","publication_status":"published","publication":"Communications in Partial Differential Equations","day":"01"},{"abstract":[{"text":"We derive lower bounds on asymptotic support propagation rates for strong solutions of the Cauchy problem for the thin-film equation. The bounds coincide up to a constant factor with the previously known upper bounds and thus are sharp. Our results hold in case of at most three spatial dimensions and n∈. (1, 2.92). The result is established using weighted backward entropy inequalities with singular weight functions to yield a differential inequality; combined with some entropy production estimates, the optimal rate of propagation is obtained. To the best of our knowledge, these are the first lower bounds on asymptotic support propagation rates for higher-order nonnegativity-preserving parabolic equations.","lang":"eng"}],"intvolume":" 255","month":"11","quality_controlled":0,"publisher":"Academic Press","publication":"Journal of Differential Equations","day":"15","year":"2013","publication_status":"published","date_created":"2018-12-11T11:51:18Z","date_published":"2013-11-15T00:00:00Z","issue":"10","doi":"10.1016/j.jde.2013.07.028","volume":255,"page":"3127 - 3149","_id":"1310","status":"public","type":"journal_article","extern":1,"citation":{"chicago":"Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation Rates for the Thin-Film Equation.” Journal of Differential Equations. Academic Press, 2013. https://doi.org/10.1016/j.jde.2013.07.028.","ista":"Fischer JL. 2013. Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. Journal of Differential Equations. 255(10), 3127–3149.","mla":"Fischer, Julian L. “Optimal Lower Bounds on Asymptotic Support Propagation Rates for the Thin-Film Equation.” Journal of Differential Equations, vol. 255, no. 10, Academic Press, 2013, pp. 3127–49, doi:10.1016/j.jde.2013.07.028.","apa":"Fischer, J. L. (2013). Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. Journal of Differential Equations. Academic Press. https://doi.org/10.1016/j.jde.2013.07.028","ama":"Fischer JL. Optimal lower bounds on asymptotic support propagation rates for the thin-film equation. Journal of Differential Equations. 2013;255(10):3127-3149. doi:10.1016/j.jde.2013.07.028","ieee":"J. L. Fischer, “Optimal lower bounds on asymptotic support propagation rates for the thin-film equation,” Journal of Differential Equations, vol. 255, no. 10. Academic Press, pp. 3127–3149, 2013.","short":"J.L. Fischer, Journal of Differential Equations 255 (2013) 3127–3149."},"date_updated":"2021-01-12T06:49:47Z","title":"Optimal lower bounds on asymptotic support propagation rates for the thin-film equation","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Julian Fischer","last_name":"Fischer"}],"publist_id":"5961"},{"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"page":"181 - 196","date_published":"2013-09-01T00:00:00Z","doi":"10.4230/LIPIcs.CSL.2013.181","date_created":"2018-12-11T11:51:39Z","has_accepted_license":"1","year":"2013","day":"01","publication":"22nd EACSL Annual Conference on Computer Science Logic","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publist_id":"5837","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Fijalkow","full_name":"Fijalkow, Nathanaël","first_name":"Nathanaël"}],"title":"Infinite-state games with finitary conditions","citation":{"mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” 22nd EACSL Annual Conference on Computer Science Logic, vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96, doi:10.4230/LIPIcs.CSL.2013.181.","short":"K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.","ieee":"K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,” in 22nd EACSL Annual Conference on Computer Science Logic, Torino, Italy, 2013, vol. 23, pp. 181–196.","apa":"Chatterjee, K., & Fijalkow, N. (2013). Infinite-state games with finitary conditions. In 22nd EACSL Annual Conference on Computer Science Logic (Vol. 23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2013.181","ama":"Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In: 22nd EACSL Annual Conference on Computer Science Logic. Vol 23. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2013:181-196. doi:10.4230/LIPIcs.CSL.2013.181","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” In 22nd EACSL Annual Conference on Computer Science Logic, 23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.181.","ista":"Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions. 22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["LIPIcs"],"month":"09","intvolume":" 23","abstract":[{"lang":"eng","text":"We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete."}],"oa_version":"Published Version","volume":23,"ec_funded":1,"publication_status":"published","file":[{"file_size":547296,"date_updated":"2020-07-14T12:44:47Z","creator":"system","file_name":"IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf","date_created":"2018-12-12T10:13:38Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5023","checksum":"b7091a3866db573c0db5ec486952255e"}],"language":[{"iso":"eng"}],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"203-09-02","end_date":"2013-09-05","location":"Torino, Italy","name":"CSL: Computer Science Logic"},"status":"public","pubrep_id":"624","series_title":"Leibniz International Proceedings in Informatics","_id":"1374","file_date_updated":"2020-07-14T12:44:47Z","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:50:14Z","ddc":["000"]},{"_id":"1385","status":"public","type":"conference","conference":{"name":"FMCAD: Formal Methods in Computer-Aided Design","start_date":"2013-10-20","end_date":"2013-10-23","location":"Portland, OR, United States"},"date_updated":"2021-01-12T06:50:19Z","department":[{"_id":"ToHe"}],"oa_version":"Preprint","abstract":[{"text":"It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results.","lang":"eng"}],"month":"12","main_file_link":[{"url":"http://arxiv.org/abs/1308.4767","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” In 2013 Formal Methods in Computer-Aided Design, 77–84. IEEE, 2013. https://doi.org/10.1109/FMCAD.2013.6679394.","ista":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple boolean functions using interpolation on a single proof. 2013 Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.","mla":"Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84, doi:10.1109/FMCAD.2013.6679394.","short":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.","ieee":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing multiple boolean functions using interpolation on a single proof,” in 2013 Formal Methods in Computer-Aided Design, Portland, OR, United States, 2013, pp. 77–84.","ama":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple boolean functions using interpolation on a single proof. In: 2013 Formal Methods in Computer-Aided Design. IEEE; 2013:77-84. doi:10.1109/FMCAD.2013.6679394","apa":"Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., & Bloem, R. (2013). Synthesizing multiple boolean functions using interpolation on a single proof. In 2013 Formal Methods in Computer-Aided Design (pp. 77–84). Portland, OR, United States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679394"},"title":"Synthesizing multiple boolean functions using interpolation on a single proof","author":[{"first_name":"Georg","full_name":"Hofferek, Georg","last_name":"Hofferek"},{"last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"full_name":"Könighofer, Bettina","last_name":"Könighofer","first_name":"Bettina"},{"full_name":"Jiang, Jie","last_name":"Jiang","first_name":"Jie"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"publist_id":"5825","external_id":{"arxiv":["1308.4767"]},"acknowledgement":"This research was supported by the European Commission through project\r\nDIAMOND (FP7-2009-IST-4-248613), and QUAINT (I774-N23), ","publisher":"IEEE","quality_controlled":"1","oa":1,"day":"11","publication":"2013 Formal Methods in Computer-Aided Design","year":"2013","doi":"10.1109/FMCAD.2013.6679394","date_published":"2013-12-11T00:00:00Z","date_created":"2018-12-11T11:51:43Z","page":"77 - 84"},{"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"citation":{"ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100.","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39212-2_11.","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013.","short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100.","apa":"Boker, U., Kuperberg, D., Kupferman, O., & Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. https://doi.org/10.1007/978-3-642-39212-2_11","ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:10.1007/978-3-642-39212-2_11","mla":"Boker, Udi, et al. Nondeterminism in the Presence of a Diverse or Unknown Future. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:10.1007/978-3-642-39212-2_11."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Boker","full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuperberg, Denis","last_name":"Kuperberg","first_name":"Denis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"},{"first_name":"Michał","last_name":"Skrzypczak","full_name":"Skrzypczak, Michał"}],"publist_id":"5823","title":"Nondeterminism in the presence of a diverse or unknown future","acknowledgement":"and ERC Grant QUALITY.","oa":1,"quality_controlled":"1","publisher":"Springer","year":"2013","has_accepted_license":"1","day":"01","page":"89 - 100","date_created":"2018-12-11T11:51:44Z","date_published":"2013-07-01T00:00:00Z","doi":"10.1007/978-3-642-39212-2_11","series_title":"Lecture Notes in Computer Science","_id":"1387","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2013-07-08","end_date":"2013-07-12","location":"Riga, Latvia"},"type":"conference","status":"public","date_updated":"2020-08-11T10:09:09Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:48Z","abstract":[{"text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 7966","month":"07","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2020-05-15T11:05:50Z","file_name":"2013_ICALP_Boker.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:48Z","file_size":276982,"checksum":"98bc02e3793072e279ec8d364b381ff3","file_id":"7857","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":7966,"issue":"PART 2"},{"title":"Positivity for Kac polynomials and DT-invariants of quivers","author":[{"first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Tamas Hausel"},{"full_name":"Letellier, Emmanuel","last_name":"Letellier","first_name":"Emmanuel"},{"last_name":"Rodríguez Villegas","full_name":"Rodríguez Villegas, Fernando","first_name":"Fernando"}],"publist_id":"5754","extern":1,"citation":{"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.","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.","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.","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Annals of Mathematics 177 (2013) 1147–1168.","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"},"date_updated":"2021-01-12T06:50:47Z","status":"public","type":"journal_article","_id":"1442","issue":"3","doi":"10.4007/annals.2013.177.3.8","volume":177,"date_published":"2013-01-01T00:00:00Z","date_created":"2018-12-11T11:52:02Z","page":"1147 - 1168","day":"01","publication":"Annals of Mathematics","year":"2013","publication_status":"published","month":"01","intvolume":" 177","quality_controlled":0,"publisher":"Princeton University Press","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1204.2375"}],"oa":1,"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\nANR-09-JCJC-0102-01. The third author is supported by the NSF grant DMS-1101484 and a Research Scholarship from the Clay Mathematical Institute.","abstract":[{"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.","lang":"eng"}]},{"page":"29 - 70","date_published":"2013-03-15T00:00:00Z","volume":25,"date_created":"2018-12-11T11:52:03Z","publication_status":"published","year":"2013","day":"15","publication":"Handbook of Moduli: Volume II","publisher":"International Press","quality_controlled":0,"alternative_title":["Advanced Lectures in Mathematics"],"main_file_link":[{"url":"http://arxiv.org/abs/1102.1717","open_access":"1"}],"oa":1,"month":"03","intvolume":" 25","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."}],"publist_id":"5753","author":[{"last_name":"Hausel","full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas"}],"title":"Global topology of the Hitchin system","date_updated":"2021-01-12T06:50:47Z","citation":{"apa":"Hausel, T. (2013). Global topology of the Hitchin system. In Handbook of Moduli: Volume II (Vol. 25, pp. 29–70). International Press.","ama":"Hausel T. Global topology of the Hitchin system. In: Handbook of Moduli: Volume II. Vol 25. International Press; 2013:29-70.","ieee":"T. Hausel, “Global topology of the Hitchin system,” in 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.","mla":"Hausel, Tamás. “Global Topology of the Hitchin System.” 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.","chicago":"Hausel, Tamás. “Global Topology of the Hitchin System.” In Handbook of Moduli: Volume II, 25:29–70. International Press, 2013."},"extern":1,"type":"book_chapter","status":"public","_id":"1443"},{"extern":1,"date_updated":"2021-01-12T06:50:57Z","citation":{"ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2013. Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. 234, 85–128.","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.","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","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Advances in Mathematics 234 (2013) 85–128.","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.","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."},"title":"Arithmetic harmonic analysis on character and quiver varieties II","author":[{"last_name":"Hausel","full_name":"Tamas Hausel","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emmanuel","full_name":"Letellier, Emmanuel","last_name":"Letellier"},{"first_name":"Fernando","full_name":"Rodríguez Villegas, Fernando","last_name":"Rodríguez Villegas"}],"publist_id":"5724","_id":"1469","status":"public","type":"journal_article","publication":"Advances in Mathematics","day":"15","publication_status":"published","year":"2013","date_created":"2018-12-11T11:52:12Z","date_published":"2013-02-15T00:00:00Z","doi":"10.1016/j.aim.2012.10.009","volume":234,"page":"85 - 128","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.","abstract":[{"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.","lang":"eng"}],"intvolume":" 234","month":"02","quality_controlled":0,"publisher":"Academic Press"},{"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\"","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."}],"month":"01","intvolume":" 7","quality_controlled":0,"publisher":"Worldwide Center of Mathematics","main_file_link":[{"url":"http://arxiv.org/abs/1012.2583","open_access":"1"}],"oa":1,"day":"01","publication":"Journal of Singularities","publication_status":"published","year":"2013","doi":"10.5427/jsing.2013.7c","volume":7,"date_published":"2013-01-01T00:00:00Z","date_created":"2018-12-11T11:52:12Z","page":"23 - 38","_id":"1470","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T06:50:58Z","citation":{"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.","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.","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.","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."},"title":"Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces","author":[{"full_name":"De Cataldo, Mark A","last_name":"De Cataldo","first_name":"Mark"},{"full_name":"Tamas Hausel","last_name":"Hausel","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","last_name":"Migliorini","full_name":"Migliorini, Luca"}],"publist_id":"5725"},{"page":"1","volume":222,"issue":"1","doi":"10.1016/j.ic.2012.11.002","date_published":"2013-01-01T00:00:00Z","date_created":"2022-08-08T11:25:34Z","publication_identifier":{"issn":["0890-5401"]},"year":"2013","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Information and Computation","quality_controlled":"1","scopus_import":"1","publisher":"Elsevier","month":"01","intvolume":" 222","oa_version":"None","author":[{"last_name":"Aceto","full_name":"Aceto, Luca","first_name":"Luca"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Sgall","full_name":"Sgall, Jiří","first_name":"Jiří"}],"article_processing_charge":"No","title":"38th International Colloquium on Automata, Languages and Programming","citation":{"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","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","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.","short":"L. Aceto, M.H. Henzinger, J. Sgall, Information and Computation 222 (2013) 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.","ista":"Aceto L, Henzinger MH, Sgall J. 2013. 38th International Colloquium on Automata, Languages and Programming. Information and Computation. 222(1), 1.","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."},"date_updated":"2023-02-23T10:09:19Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_type":"letter_note","status":"public","_id":"11758"},{"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","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."}],"intvolume":" 140","month":"04","publisher":"Company of Biologists","quality_controlled":0,"publication":"Development","day":"18","year":"2013","publication_status":"published","date_created":"2018-12-11T11:53:41Z","volume":140,"issue":"8","date_published":"2013-04-18T00:00:00Z","doi":"10.1242/dev.092726","page":"1740 - 1750","_id":"1726","status":"public","type":"journal_article","extern":1,"citation":{"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.","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.","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","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","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.","short":"N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140 (2013) 1740–1750."},"date_updated":"2021-01-12T06:52:47Z","title":"The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling","author":[{"first_name":"Nitza","last_name":"Kahane","full_name":"Kahane, Nitza"},{"first_name":"Vanessa","last_name":"Ribes","full_name":"Ribes, Vanessa"},{"orcid":"0000-0003-4509-4998","full_name":"Anna Kicheva","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"last_name":"Kalcheim","full_name":"Kalcheim, Chaya","first_name":"Chaya"}],"publist_id":"5402"},{"month":"05","intvolume":" 8","publisher":"Cold Spring Harbor Laboratory Press","quality_controlled":0,"abstract":[{"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.","lang":"eng"}],"issue":"5","doi":"10.1101/pdb.top074237","date_published":"2013-05-01T00:00:00Z","volume":8,"date_created":"2018-12-11T11:53:41Z","page":"387 - 403","day":"01","publication":"Cold Spring Harbor Protocols","publication_status":"published","year":"2013","status":"public","type":"journal_article","_id":"1727","title":"Quantitative imaging of morphogen gradients in drosophila imaginal discs","publist_id":"5401","author":[{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","orcid":"0000-0003-4509-4998","last_name":"Kicheva"},{"first_name":"Laurent","full_name":"Holtzer, Laurent","last_name":"Holtzer"},{"first_name":"Ortrud","full_name":"Wartlick, Ortrud","last_name":"Wartlick"},{"first_name":"Thomas","last_name":"Schmidt","full_name":"Schmidt, Thomas S"},{"first_name":"Marcos","last_name":"González Gaitán","full_name":"González-Gaitán, Marcos A"}],"extern":1,"citation":{"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.","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.","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","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","short":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold Spring Harbor Protocols 8 (2013) 387–403.","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.","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."},"date_updated":"2021-01-12T06:52:47Z"},{"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","abstract":[{"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.","lang":"eng"}],"month":"01","intvolume":" 103","publisher":"American Institute of Physics","quality_controlled":0,"main_file_link":[{"url":"http://arxiv.org/abs/1307.7196","open_access":"1"}],"oa":1,"day":"23","publication":"Applied Physics Letters","publication_status":"published","year":"2013","date_published":"2013-01-23T00:00:00Z","issue":"26","volume":103,"doi":"10.1063/1.4858959","date_created":"2018-12-11T11:53:52Z","_id":"1760","status":"public","type":"journal_article","extern":1,"citation":{"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.","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).","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.","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","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"},"date_updated":"2021-01-12T06:53:02Z","title":"SiGe quantum dots for fast hole spin Rabi oscillations","author":[{"first_name":"Natalia","full_name":"Ares, Natalia","last_name":"Ares"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Georgios Katsaros"},{"last_name":"Golovach","full_name":"Golovach, Vitaly N","first_name":"Vitaly"},{"first_name":"Jianjun","last_name":"Zhang","full_name":"Zhang, Jianjun"},{"first_name":"Aaron","last_name":"Prager","full_name":"Prager, Aaron A"},{"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","last_name":"De Franceschi","full_name":"De Franceschi, Silvano"}],"publist_id":"5364"},{"publist_id":"5365","author":[{"first_name":"Natalia","last_name":"Ares","full_name":"Ares, Natalia"},{"first_name":"Vitaly","full_name":"Golovach, Vitaly N","last_name":"Golovach"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Georgios Katsaros"},{"last_name":"Stoffel","full_name":"Stoffel, Mathieu","first_name":"Mathieu"},{"first_name":"Frank","last_name":"Fournel","full_name":"Fournel, Frank"},{"first_name":"Leonid","last_name":"Glazman","full_name":"Glazman, Leonid I"},{"full_name":"Schmidt, Oliver G","last_name":"Schmidt","first_name":"Oliver"},{"last_name":"De Franceschi","full_name":"De Franceschi, Silvano","first_name":"Silvano"}],"title":"Nature of tunable hole g factors in quantum dots","citation":{"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.","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","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","short":"N. Ares, V. Golovach, G. Katsaros, M. Stoffel, F. Fournel, L. Glazman, O. Schmidt, S. De Franceschi, Physical Review Letters 110 (2013).","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.","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.","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)."},"date_updated":"2021-01-12T06:53:01Z","extern":1,"type":"journal_article","status":"public","_id":"1759","volume":110,"issue":"4","date_published":"2013-01-23T00:00:00Z","doi":"10.1103/PhysRevLett.110.046602","date_created":"2018-12-11T11:53:51Z","publication_status":"published","year":"2013","day":"23","publication":"Physical Review Letters","publisher":"American Physical Society","quality_controlled":0,"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.0476"}],"month":"01","intvolume":" 110","abstract":[{"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.","lang":"eng"}],"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"},{"status":"public","type":"journal_article","_id":"1785","title":"Experimental realization of non-Abelian non-adiabatic geometric gates","publist_id":"5329","author":[{"first_name":"Abdufarrukh","full_name":"Abdumalikov, Abdufarrukh A","last_name":"Abdumalikov"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Johannes Fink","last_name":"Fink"},{"first_name":"K","full_name":"Juliusson, K","last_name":"Juliusson"},{"first_name":"M","last_name":"Pechal","full_name":"Pechal, M"},{"full_name":"Berger, Stefan T","last_name":"Berger","first_name":"Stefan"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"},{"first_name":"Stefan","full_name":"Filipp, Stefan","last_name":"Filipp"}],"extern":1,"citation":{"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.","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.","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.","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."},"date_updated":"2021-01-12T06:53:11Z","intvolume":" 496","month":"04","publisher":"Nature Publishing Group","quality_controlled":0,"acknowledgement":"This work is supported financially by GEOMDISS, the Swiss National Science Foundation and ETH Zurich","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."}],"date_created":"2018-12-11T11:54:00Z","date_published":"2013-04-25T00:00:00Z","volume":496,"issue":"7446","doi":"10.1038/nature12010","page":"482 - 485","publication":"Nature","day":"25","year":"2013","publication_status":"published"},{"type":"journal_article","status":"public","_id":"1787","author":[{"first_name":"C","last_name":"Lang","full_name":"Lang, C"},{"first_name":"Christopher","last_name":"Eichler","full_name":"Eichler, Christopher"},{"first_name":"L.","full_name":"Steffen, L. Kraig","last_name":"Steffen"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Johannes Fink"},{"full_name":"Woolley, Matthew J","last_name":"Woolley","first_name":"Matthew"},{"first_name":"Alexandre","full_name":"Blais, Alexandre","last_name":"Blais"},{"first_name":"Andreas","full_name":"Wallraff, Andreas","last_name":"Wallraff"}],"publist_id":"5327","title":"Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies","date_updated":"2021-01-12T06:53:11Z","citation":{"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.","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.","short":"C. Lang, C. Eichler, L. Steffen, J.M. Fink, M. Woolley, A. Blais, A. Wallraff, Nature Physics 9 (2013) 345–348.","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","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."},"extern":1,"publisher":"Nature Publishing Group","quality_controlled":0,"month":"06","intvolume":" 9","abstract":[{"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.","lang":"eng"}],"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","page":"345 - 348","doi":"10.1038/nphys2612","date_published":"2013-06-01T00:00:00Z","issue":"6","volume":9,"date_created":"2018-12-11T11:54:00Z","publication_status":"published","year":"2013","day":"01","publication":"Nature Physics"},{"title":"Collective suppression of linewidths in circuit QED","publist_id":"5328","author":[{"first_name":"Felix","last_name":"Nissen","full_name":"Nissen, Felix"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","last_name":"Fink"},{"last_name":"Mlynek","full_name":"Mlynek, Jonas A","first_name":"Jonas"},{"last_name":"Wallraff","full_name":"Wallraff, Andreas","first_name":"Andreas"},{"first_name":"Jonathan","full_name":"Keeling, Jonathan M","last_name":"Keeling"}],"extern":1,"citation":{"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.","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).","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.","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"},"date_updated":"2021-01-12T06:53:11Z","status":"public","type":"journal_article","_id":"1786","volume":110,"doi":"10.1103/PhysRevLett.110.203602","issue":"20","date_published":"2013-05-15T00:00:00Z","date_created":"2018-12-11T11:54:00Z","day":"15","publication":"Physical Review Letters","year":"2013","publication_status":"published","month":"05","intvolume":" 110","publisher":"American Physical Society","quality_controlled":0,"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1302.0665"}],"acknowledgement":"J. K. acknowledges financial support from EPSRC program “TOPNES” (EP/I031014/1) and EPSRC (EP/G004714/2)","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."}]},{"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."}],"month":"10","intvolume":" 80","quality_controlled":0,"publisher":"Elsevier","day":"02","publication":"Neuron","year":"2013","publication_status":"published","volume":80,"issue":"1","date_published":"2013-10-02T00:00:00Z","doi":"10.1016/j.neuron.2013.09.019","date_created":"2018-12-11T11:54:01Z","page":"9 - 11","_id":"1790","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T06:53:13Z","citation":{"ista":"Novarino G, Baek S, Gleeson J. 2013. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 80(1), 9–11.","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.","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","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.","short":"G. Novarino, S. Baek, J. Gleeson, Neuron 80 (2013) 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."},"title":"The sacred disease: The puzzling genetics of epileptic disorders","publist_id":"5323","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Gaia Novarino","last_name":"Novarino"},{"first_name":"Seungtae","last_name":"Baek","full_name":"Baek, SeungTae"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph G"}]},{"day":"01","publication":"Biochemical Society Transactions","publication_status":"published","year":"2013","date_published":"2013-10-01T00:00:00Z","doi":"10.1042/BST20130193","volume":41,"issue":"5","date_created":"2018-12-11T11:55:00Z","page":"1265 - 1271","acknowledgement":"This work was funded by the Medical Research Council.","abstract":[{"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.","lang":"eng"}],"month":"10","intvolume":" 41","quality_controlled":0,"publisher":"Portland Press","extern":1,"date_updated":"2021-01-12T06:54:28Z","citation":{"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.","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.","short":"L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271.","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","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","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.","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."},"title":"A long road towards the structure of respiratory complex I, a giant molecular proton pump","publist_id":"5106","author":[{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989"},{"last_name":"Baradaran","full_name":"Baradaran, Rozbeh ","first_name":"Rozbeh"},{"first_name":"Rouslan","full_name":"Efremov, Rouslan G","last_name":"Efremov"},{"full_name":"Berrisford, John M","last_name":"Berrisford","first_name":"John"},{"first_name":"Gurdeep","last_name":"Minhas","full_name":"Minhas, Gurdeep S"}],"_id":"1977","status":"public","type":"journal_article"},{"quality_controlled":0,"publisher":"Nature Publishing Group","month":"02","intvolume":" 494","abstract":[{"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.","lang":"eng"}],"acknowledgement":"This work was funded by the Medical Research Council.","page":"443 - 448","volume":494,"doi":"10.1038/nature11871","issue":"7438","date_published":"2013-02-28T00:00:00Z","date_created":"2018-12-11T11:55:01Z","publication_status":"published","year":"2013","day":"28","publication":"Nature","type":"journal_article","status":"public","_id":"1978","author":[{"first_name":"Rozbeh","last_name":"Baradaran","full_name":"Baradaran, Rozbeh "},{"last_name":"Berrisford","full_name":"Berrisford, John M","first_name":"John"},{"last_name":"Minhas","full_name":"Minhas, Gurdeep S","first_name":"Gurdeep"},{"full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5107","title":"Crystal structure of the entire respiratory complex i","citation":{"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.","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.","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","short":"R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.","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."},"date_updated":"2021-01-12T06:54:28Z","extern":1},{"extern":1,"date_updated":"2021-01-12T06:54:33Z","citation":{"short":"B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.","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.","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","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","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.","ista":"Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335.","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."},"title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","author":[{"orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Doris","full_name":"Bachtrog, Doris","last_name":"Bachtrog"}],"publist_id":"5092","_id":"1991","status":"public","type":"journal_article","day":"18","publication":"Nature","publication_status":"published","year":"2013","doi":"10.1038/nature12235","date_published":"2013-07-18T00:00:00Z","volume":499,"issue":"7458","date_created":"2018-12-11T11:55:05Z","page":"332 - 335","acknowledgement":"Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B.","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."}],"month":"07","intvolume":" 499","publisher":"Nature Publishing Group","quality_controlled":0},{"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."}],"month":"12","intvolume":" 9","quality_controlled":0,"publisher":"Public Library of Science","day":"01","publication":"PLoS Computational Biology","year":"2013","publication_status":"published","date_published":"2013-12-01T00:00:00Z","volume":9,"issue":"12","doi":"10.1371/journal.pcbi.1003347","date_created":"2018-12-11T11:55:04Z","_id":"1988","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T06:54:32Z","citation":{"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).","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.","short":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013).","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","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","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."},"title":"Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation","publist_id":"5095","author":[{"full_name":"Bonny, Mike ","last_name":"Bonny","first_name":"Mike"},{"full_name":"Fischer-Friedrich, Elisabeth","last_name":"Fischer Friedrich","first_name":"Elisabeth"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Martin Loose","last_name":"Loose"},{"first_name":"Petra","full_name":"Schwille, Petra ","last_name":"Schwille"},{"first_name":"Karsten","last_name":"Kruse","full_name":"Kruse, Karsten"}]},{"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1214/12-AOS1080"}],"scopus_import":1,"intvolume":" 41","month":"04","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."}],"oa_version":"Published Version","volume":41,"issue":"2","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"2010","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:42Z","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","page":"436 - 463","date_created":"2018-12-11T11:55:11Z","date_published":"2013-04-01T00:00:00Z","doi":"10.1214/12-AOS1080","year":"2013","publication":"The Annals of Statistics","day":"01","external_id":{"arxiv":["1207.0547"]},"author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216"},{"full_name":"Raskutti, Garvesh","last_name":"Raskutti","first_name":"Garvesh"},{"full_name":"Bühlmann, Peter","last_name":"Bühlmann","first_name":"Peter"},{"last_name":"Yu","full_name":"Yu, Bin","first_name":"Bin"}],"publist_id":"5066","title":"Geometry of the faithfulness assumption in causal inference","citation":{"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.","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","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"author":[{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler"},{"last_name":"Slavkovic","full_name":"Slavkovic, Aleksandra","first_name":"Aleksandra"},{"last_name":"Fienberg","full_name":"Fienberg, Stephen","first_name":"Stephen"}],"publist_id":"5067","article_processing_charge":"No","title":"Privacy-preserving data sharing for genome-wide association studies","department":[{"_id":"CaUh"}],"citation":{"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.","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.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality 5 (2013) 137–166.","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","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","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."},"date_updated":"2021-01-12T06:54:41Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2009","page":"137 - 166","issue":"1","date_published":"2013-08-01T00:00:00Z","volume":5,"doi":"10.29012/jpc.v5i1.629","date_created":"2018-12-11T11:55:11Z","year":"2013","publication_status":"published","day":"01","publication":"Journal of Privacy and Confidentiality ","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Carnegie Mellon University","main_file_link":[{"url":"http://repository.cmu.edu/jpc/vol5/iss1/6","open_access":"1"}],"oa":1,"month":"08","intvolume":" 5","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution","publist_id":"4964","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Beatriz Vicoso","orcid":"0000-0002-4579-8306"},{"first_name":"Vera","full_name":"Kaiser, Vera B","last_name":"Kaiser"},{"last_name":"Bachtrog","full_name":"Bachtrog, Doris","first_name":"Doris"}],"extern":1,"date_updated":"2021-01-12T06:55:08Z","citation":{"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.","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.","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.","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","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"},"status":"public","type":"journal_article","_id":"2074","volume":110,"issue":"16","date_published":"2013-04-16T00:00:00Z","doi":"10.1073/pnas.1217027110","date_created":"2018-12-11T11:55:33Z","page":"6453 - 6458","day":"16","publication":"PNAS","publication_status":"published","year":"2013","month":"04","intvolume":" 110","quality_controlled":0,"publisher":"National Academy of Sciences","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. "}]}]