--- _id: '1013' abstract: - lang: eng text: From microwave ovens to satellite television to the GPS and data services on our mobile phones, microwave technology is everywhere today. But one technology that has so far failed to prove its worth in this wavelength regime is quantum communication that uses the states of single photons as information carriers. This is because single microwave photons, as opposed to classical microwave signals, are extremely vulnerable to noise from thermal excitations in the channels through which they travel. Two new independent studies, one by Ze-Liang Xiang at Technische Universität Wien (Vienna), Austria, and colleagues [1] and another by Benoît Vermersch at the University of Innsbruck, also in Austria, and colleagues [2] now describe a theoretical protocol for microwave quantum communication that is resilient to thermal and other types of noise. Their approach could become a powerful technique to establish fast links between superconducting data processors in a future all-microwave quantum network. article_processing_charge: No article_type: review author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: 'Fink JM. Viewpoint: Microwave quantum states beat the heat. Physics. 2017;10(32). doi:10.1103/Physics.10.32' apa: 'Fink, J. M. (2017). Viewpoint: Microwave quantum states beat the heat. Physics. American Physical Society. https://doi.org/10.1103/Physics.10.32' chicago: 'Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics. American Physical Society, 2017. https://doi.org/10.1103/Physics.10.32.' ieee: 'J. M. Fink, “Viewpoint: Microwave quantum states beat the heat,” Physics, vol. 10, no. 32. American Physical Society, 2017.' ista: 'Fink JM. 2017. Viewpoint: Microwave quantum states beat the heat. Physics. 10(32).' mla: 'Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics, vol. 10, no. 32, American Physical Society, 2017, doi:10.1103/Physics.10.32.' short: J.M. Fink, Physics 10 (2017). date_created: 2018-12-11T11:49:41Z date_published: 2017-03-27T00:00:00Z date_updated: 2022-06-07T10:58:31Z day: '27' ddc: - '530' department: - _id: JoFi doi: 10.1103/Physics.10.32 file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-10-24T11:38:14Z date_updated: 2019-10-24T11:38:14Z file_id: '6968' file_name: 2017_Physics_Fink.pdf file_size: 193622 relation: main_file success: 1 file_date_updated: 2019-10-24T11:38:14Z has_accepted_license: '1' intvolume: ' 10' issue: '32' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Physics publication_status: published publisher: American Physical Society publist_id: '6382' quality_controlled: '1' status: public title: 'Viewpoint: Microwave quantum states beat the heat' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2017' ... --- _id: '10126' article_number: 391a article_processing_charge: No article_type: letter_note author: - first_name: Afshin full_name: Vahid Belarghou, Afshin last_name: Vahid Belarghou - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Timon full_name: Idema, Timon last_name: Idema citation: ama: Vahid Belarghou A, Šarić A, Idema T. Curvature mediated interactions in highly curved membranes. Biophysical Journal. 2017;112(3). doi:10.1016/j.bpj.2016.11.2123 apa: Vahid Belarghou, A., Šarić, A., & Idema, T. (2017). Curvature mediated interactions in highly curved membranes. Biophysical Journal. Elsevier . https://doi.org/10.1016/j.bpj.2016.11.2123 chicago: Vahid Belarghou, Afshin, Anđela Šarić, and Timon Idema. “Curvature Mediated Interactions in Highly Curved Membranes.” Biophysical Journal. Elsevier , 2017. https://doi.org/10.1016/j.bpj.2016.11.2123. ieee: A. Vahid Belarghou, A. Šarić, and T. Idema, “Curvature mediated interactions in highly curved membranes,” Biophysical Journal, vol. 112, no. 3. Elsevier , 2017. ista: Vahid Belarghou A, Šarić A, Idema T. 2017. Curvature mediated interactions in highly curved membranes. Biophysical Journal. 112(3), 391a. mla: Vahid Belarghou, Afshin, et al. “Curvature Mediated Interactions in Highly Curved Membranes.” Biophysical Journal, vol. 112, no. 3, 391a, Elsevier , 2017, doi:10.1016/j.bpj.2016.11.2123. short: A. Vahid Belarghou, A. Šarić, T. Idema, Biophysical Journal 112 (2017). date_created: 2021-10-12T07:47:55Z date_published: 2017-02-03T00:00:00Z date_updated: 2021-11-03T10:02:45Z day: '03' doi: 10.1016/j.bpj.2016.11.2123 extern: '1' intvolume: ' 112' issue: '3' keyword: - biophysics language: - iso: eng main_file_link: - open_access: '1' url: https://www.cell.com/biophysj/fulltext/S0006-3495(16)33153-8 month: '02' oa: 1 oa_version: Published Version publication: Biophysical Journal publication_identifier: issn: - 0006-3495 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Curvature mediated interactions in highly curved membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 112 year: '2017' ... --- _id: '10175' abstract: - lang: eng text: We study periodic homogenization by Γ-convergence of integral functionals with integrands W(x,ξ) having no polynomial growth and which are both not necessarily continuous with respect to the space variable and not necessarily convex with respect to the matrix variable. This allows to deal with homogenization of composite hyperelastic materials consisting of two or more periodic components whose the energy densities tend to infinity as the volume of matter tends to zero, i.e., W(x,ξ)=∑j∈J1Vj(x)Hj(ξ) where {Vj}j∈J is a finite family of open disjoint subsets of RN, with |∂Vj|=0 for all j∈J and ∣∣RN∖⋃j∈JVj|=0, and, for each j∈J, Hj(ξ)→∞ as detξ→0. In fact, our results apply to integrands of type W(x,ξ)=a(x)H(ξ) when H(ξ)→∞ as detξ→0 and a∈L∞(RN;[0,∞[) is 1-periodic and is either continuous almost everywhere or not continuous. When a is not continuous, we obtain a density homogenization formula which is a priori different from the classical one by Braides–Müller. Although applications to hyperelasticity are limited due to the fact that our framework is not consistent with the constraint of noninterpenetration of the matter, our results can be of technical interest to analysis of homogenization of integral functionals. article_processing_charge: No article_type: original author: - first_name: Omar full_name: Anza Hafsa, Omar last_name: Anza Hafsa - first_name: Nicolas full_name: Clozeau, Nicolas id: fea1b376-906f-11eb-847d-b2c0cf46455b last_name: Clozeau - first_name: Jean-Philippe full_name: Mandallena, Jean-Philippe last_name: Mandallena citation: ama: Anza Hafsa O, Clozeau N, Mandallena J-P. Homogenization of nonconvex unbounded singular integrals. Annales mathématiques Blaise Pascal. 2017;24(2):135-193. doi:10.5802/ambp.367 apa: Anza Hafsa, O., Clozeau, N., & Mandallena, J.-P. (2017). Homogenization of nonconvex unbounded singular integrals. Annales Mathématiques Blaise Pascal. Université Clermont Auvergne. https://doi.org/10.5802/ambp.367 chicago: Anza Hafsa, Omar, Nicolas Clozeau, and Jean-Philippe Mandallena. “Homogenization of Nonconvex Unbounded Singular Integrals.” Annales Mathématiques Blaise Pascal. Université Clermont Auvergne, 2017. https://doi.org/10.5802/ambp.367. ieee: O. Anza Hafsa, N. Clozeau, and J.-P. Mandallena, “Homogenization of nonconvex unbounded singular integrals,” Annales mathématiques Blaise Pascal, vol. 24, no. 2. Université Clermont Auvergne, pp. 135–193, 2017. ista: Anza Hafsa O, Clozeau N, Mandallena J-P. 2017. Homogenization of nonconvex unbounded singular integrals. Annales mathématiques Blaise Pascal. 24(2), 135–193. mla: Anza Hafsa, Omar, et al. “Homogenization of Nonconvex Unbounded Singular Integrals.” Annales Mathématiques Blaise Pascal, vol. 24, no. 2, Université Clermont Auvergne, 2017, pp. 135–93, doi:10.5802/ambp.367. short: O. Anza Hafsa, N. Clozeau, J.-P. Mandallena, Annales Mathématiques Blaise Pascal 24 (2017) 135–193. date_created: 2021-10-23T10:54:23Z date_published: 2017-11-20T00:00:00Z date_updated: 2021-10-28T15:16:25Z day: '20' ddc: - '510' doi: 10.5802/ambp.367 extern: '1' file: - access_level: open_access checksum: 18f40d13dc5d1e24438260b1875b886f content_type: application/pdf creator: cziletti date_created: 2021-10-28T15:02:56Z date_updated: 2021-10-28T15:02:56Z file_id: '10194' file_name: 2017_AMBP_AnzaHafsa.pdf file_size: 850726 relation: main_file success: 1 file_date_updated: 2021-10-28T15:02:56Z has_accepted_license: '1' intvolume: ' 24' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/3.0/ month: '11' oa: 1 oa_version: Published Version page: 135-193 publication: Annales mathématiques Blaise Pascal publication_identifier: eissn: - 2118-7436 issn: - 1259-1734 publication_status: published publisher: Université Clermont Auvergne quality_controlled: '1' status: public title: Homogenization of nonconvex unbounded singular integrals tmp: image: /images/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/3.0/legalcode name: Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0) short: CC BY-ND (3.0) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 24 year: '2017' ... --- _id: '103' abstract: - lang: eng text: We investigate effects of quasiparticle poisoning in a Majorana island with strong tunnel coupling to normal-metal leads. In addition to the main Coulomb blockade diamonds, "shadow" diamonds appear, shifted by 1e in gate voltage, consistent with transport through an excited (poisoned) state of the island. Comparison to a simple model yields an estimate of parity lifetime for the strongly coupled island (∼1 μs) and sets a bound for a weakly coupled island (>10 μs). Fluctuations in the gate-voltage spacing of Coulomb peaks at high field, reflecting Majorana hybridization, are enhanced by the reduced lever arm at strong coupling. When converted from gate voltage to energy units, fluctuations are consistent with previous measurements. acknowledgement: Research supported by Microsoft, the Danish National Research Foundation, the Lundbeck Foundation, Carlsberg Foundation, Villum Foundation, and the European Commission. article_number: '137701' author: - first_name: S M full_name: Albrecht, S M last_name: Albrecht - first_name: Esben full_name: Hansen, Esben last_name: Hansen - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth - first_name: Thomas full_name: Jespersen, Thomas last_name: Jespersen - first_name: Jesper full_name: Nygård, Jesper last_name: Nygård - first_name: Peter full_name: Krogstrup, Peter last_name: Krogstrup - first_name: Jeroen full_name: Danon, Jeroen last_name: Danon - first_name: Karsten full_name: Flensberg, Karsten last_name: Flensberg - first_name: Charles full_name: Marcus, Charles last_name: Marcus citation: ama: Albrecht SM, Hansen E, Higginbotham AP, et al. Transport signatures of quasiparticle poisoning in a majorana island. APS Physics, Physical Review Letters. 2017;118(13). doi:10.1103/PhysRevLett.118.137701 apa: Albrecht, S. M., Hansen, E., Higginbotham, A. P., Kuemmeth, F., Jespersen, T., Nygård, J., … Marcus, C. (2017). Transport signatures of quasiparticle poisoning in a majorana island. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.137701 chicago: Albrecht, S M, Esben Hansen, Andrew P Higginbotham, Ferdinand Kuemmeth, Thomas Jespersen, Jesper Nygård, Peter Krogstrup, Jeroen Danon, Karsten Flensberg, and Charles Marcus. “Transport Signatures of Quasiparticle Poisoning in a Majorana Island.” APS Physics, Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.137701. ieee: S. M. Albrecht et al., “Transport signatures of quasiparticle poisoning in a majorana island,” APS Physics, Physical Review Letters, vol. 118, no. 13. American Physical Society, 2017. ista: Albrecht SM, Hansen E, Higginbotham AP, Kuemmeth F, Jespersen T, Nygård J, Krogstrup P, Danon J, Flensberg K, Marcus C. 2017. Transport signatures of quasiparticle poisoning in a majorana island. APS Physics, Physical Review Letters. 118(13), 137701. mla: Albrecht, S. M., et al. “Transport Signatures of Quasiparticle Poisoning in a Majorana Island.” APS Physics, Physical Review Letters, vol. 118, no. 13, 137701, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.137701. short: S.M. Albrecht, E. Hansen, A.P. Higginbotham, F. Kuemmeth, T. Jespersen, J. Nygård, P. Krogstrup, J. Danon, K. Flensberg, C. Marcus, APS Physics, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:44:39Z date_published: 2017-03-31T00:00:00Z date_updated: 2021-01-12T06:47:47Z day: '31' doi: 10.1103/PhysRevLett.118.137701 extern: '1' external_id: arxiv: - '1612.05748' intvolume: ' 118' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.05748 month: '03' oa: 1 oa_version: Preprint publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7951' quality_controlled: '1' status: public title: Transport signatures of quasiparticle poisoning in a majorana island type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2017' ... --- _id: '10370' abstract: - lang: eng text: Eukaryotic cells are densely packed with macromolecular complexes and intertwining organelles, continually transported and reshaped. Intriguingly, organelles avoid clashing and entangling with each other in such limited space. Mitochondria form extensive networks constantly remodeled by fission and fusion. Here, we show that mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of mitochondria – via encounter with motile intracellular pathogens, via external pressure applied by an atomic force microscope, or via cell migration across uneven microsurfaces – results in the recruitment of the mitochondrial fission machinery, and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria, acts as a membrane-bound force sensor to recruit the fission machinery to mechanically strained sites. Thus, mitochondria adapt to the environment by sensing and responding to biomechanical cues. Our findings that mechanical triggers can be coupled to biochemical responses in membrane dynamics may explain how organelles orderly cohabit in the crowded cytoplasm. article_number: e30292 article_processing_charge: No article_type: original author: - first_name: Sebastian Carsten Johannes full_name: Helle, Sebastian Carsten Johannes last_name: Helle - first_name: Qian full_name: Feng, Qian last_name: Feng - first_name: Mathias J full_name: Aebersold, Mathias J last_name: Aebersold - first_name: Luca full_name: Hirt, Luca last_name: Hirt - first_name: Raphael R full_name: Grüter, Raphael R last_name: Grüter - first_name: Afshin full_name: Vahid, Afshin last_name: Vahid - first_name: Andrea full_name: Sirianni, Andrea last_name: Sirianni - first_name: Serge full_name: Mostowy, Serge last_name: Mostowy - first_name: Jess G full_name: Snedeker, Jess G last_name: Snedeker - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Timon full_name: Idema, Timon last_name: Idema - first_name: Tomaso full_name: Zambelli, Tomaso last_name: Zambelli - first_name: Benoît full_name: Kornmann, Benoît last_name: Kornmann citation: ama: Helle SCJ, Feng Q, Aebersold MJ, et al. Mechanical force induces mitochondrial fission. eLife. 2017;6. doi:10.7554/elife.30292 apa: Helle, S. C. J., Feng, Q., Aebersold, M. J., Hirt, L., Grüter, R. R., Vahid, A., … Kornmann, B. (2017). Mechanical force induces mitochondrial fission. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30292 chicago: Helle, Sebastian Carsten Johannes, Qian Feng, Mathias J Aebersold, Luca Hirt, Raphael R Grüter, Afshin Vahid, Andrea Sirianni, et al. “Mechanical Force Induces Mitochondrial Fission.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30292. ieee: S. C. J. Helle et al., “Mechanical force induces mitochondrial fission,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. 2017. Mechanical force induces mitochondrial fission. eLife. 6, e30292. mla: Helle, Sebastian Carsten Johannes, et al. “Mechanical Force Induces Mitochondrial Fission.” ELife, vol. 6, e30292, eLife Sciences Publications, 2017, doi:10.7554/elife.30292. short: S.C.J. Helle, Q. Feng, M.J. Aebersold, L. Hirt, R.R. Grüter, A. Vahid, A. Sirianni, S. Mostowy, J.G. Snedeker, A. Šarić, T. Idema, T. Zambelli, B. Kornmann, ELife 6 (2017). date_created: 2021-11-29T08:51:38Z date_published: 2017-11-09T00:00:00Z date_updated: 2021-11-29T09:28:14Z day: '09' ddc: - '572' doi: 10.7554/elife.30292 extern: '1' external_id: pmid: - '29119945' file: - access_level: open_access checksum: c35f42dcfb007f6d6c761a27e24c26d3 content_type: application/pdf creator: cchlebak date_created: 2021-11-29T09:07:41Z date_updated: 2021-11-29T09:07:41Z file_id: '10372' file_name: 2017_eLife_Helle.pdf file_size: 6120157 relation: main_file success: 1 file_date_updated: 2021-11-29T09:07:41Z has_accepted_license: '1' intvolume: ' 6' keyword: - general immunology and microbiology - general biochemistry - genetics and molecular biology - general medicine - general neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://elifesciences.org/articles/30292 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Mechanical force induces mitochondrial fission tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2017' ... --- _id: '10369' abstract: - lang: eng text: Biological membranes have a central role in mediating the organization of membrane-curving proteins, a dynamic process that has proven to be challenging to probe experimentally. Using atomic force microscopy, we capture the hierarchically organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid membranes. Their structure reveals distinct long linear aggregates of proteins, regularly spaced by up to 300 nm. Employing accurate free-energy calculations from large-scale coarse-grained computer simulations, we found that the membrane mediates the interaction among protein filaments as a combination of short- and long-ranged interactions. The long-ranged component acts at strikingly long distances, giving rise to a variety of micron-sized ordered patterns. This mechanism may contribute to the long-ranged spatiotemporal control of membrane remodeling by proteins in the cell. acknowledgement: M.S. and G.A.V. acknowledge their research reported in this publication as being supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01-GM063796. Computational resources were provided to M.S. and G.A.V. by the National Science Foundation through XSEDE (Grant TG-MCA94P017, supercomputers Stampede and Gordon), and also by the Blue Waters computing project at the National Center for Supercomputing Applications (University of Illinois at Urbana–Champaign, NSF Awards OCI-0725070 and ACI-1238993). A.Š. acknowledges support from the Human Frontier Science Program and Royal Society. J.M.H. and K.Y.C.L. acknowledge the support from the National Science Foundation (Grant MCB-1413613) and the NSF-supported MRSEC program at the University of Chicago (Grant DMR-1420709). We are grateful to Carsten Mim and Vinzenz Unger of Northwestern University for generously providing us with the protein. We thank all the members of the Voth group for fruitful discussions, especially John M. A. Grime. article_processing_charge: No article_type: original author: - first_name: Mijo full_name: Simunovic, Mijo last_name: Simunovic - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: J. Michael full_name: Henderson, J. Michael last_name: Henderson - first_name: Ka Yee C. full_name: Lee, Ka Yee C. last_name: Lee - first_name: Gregory A. full_name: Voth, Gregory A. last_name: Voth citation: ama: Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-range organization of membrane-curving proteins. ACS Central Science. 2017;3(12):1246-1253. doi:10.1021/acscentsci.7b00392 apa: Simunovic, M., Šarić, A., Henderson, J. M., Lee, K. Y. C., & Voth, G. A. (2017). Long-range organization of membrane-curving proteins. ACS Central Science. American Chemical Society. https://doi.org/10.1021/acscentsci.7b00392 chicago: Simunovic, Mijo, Anđela Šarić, J. Michael Henderson, Ka Yee C. Lee, and Gregory A. Voth. “Long-Range Organization of Membrane-Curving Proteins.” ACS Central Science. American Chemical Society, 2017. https://doi.org/10.1021/acscentsci.7b00392. ieee: M. Simunovic, A. Šarić, J. M. Henderson, K. Y. C. Lee, and G. A. Voth, “Long-range organization of membrane-curving proteins,” ACS Central Science, vol. 3, no. 12. American Chemical Society, pp. 1246–1253, 2017. ista: Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. 2017. Long-range organization of membrane-curving proteins. ACS Central Science. 3(12), 1246–1253. mla: Simunovic, Mijo, et al. “Long-Range Organization of Membrane-Curving Proteins.” ACS Central Science, vol. 3, no. 12, American Chemical Society, 2017, pp. 1246–53, doi:10.1021/acscentsci.7b00392. short: M. Simunovic, A. Šarić, J.M. Henderson, K.Y.C. Lee, G.A. Voth, ACS Central Science 3 (2017) 1246–1253. date_created: 2021-11-29T08:49:50Z date_published: 2017-11-21T00:00:00Z date_updated: 2021-11-29T09:28:06Z day: '21' ddc: - '540' doi: 10.1021/acscentsci.7b00392 extern: '1' external_id: pmid: - '29296664' file: - access_level: open_access checksum: 1cf3e5e5342f2d728f47560acc3ec560 content_type: application/pdf creator: cchlebak date_created: 2021-11-29T09:00:40Z date_updated: 2021-11-29T09:00:40Z file_id: '10371' file_name: 2017_ACSCentSci_Simunovic.pdf file_size: 2635263 relation: main_file success: 1 file_date_updated: 2021-11-29T09:00:40Z has_accepted_license: '1' intvolume: ' 3' issue: '12' keyword: - general chemical engineering - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://pubs.acs.org/doi/10.1021/acscentsci.7b00392 month: '11' oa: 1 oa_version: Published Version page: 1246-1253 pmid: 1 publication: ACS Central Science publication_identifier: eissn: - 2374-7951 issn: - 2374-7943 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Long-range organization of membrane-curving proteins tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 3 year: '2017' ... --- _id: '10373' abstract: - lang: eng text: 'Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis.' acknowledgement: P.W. acknowledges many invaluable discussions with Martin Neumann, Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge financial support from the Austrian Academy of Sciences through a doctoral (DOC) fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results presented here have been achieved in part using the Vienna Scientific Cluster. article_processing_charge: No article_type: original author: - first_name: Peter full_name: Wirnsberger, Peter last_name: Wirnsberger - first_name: Domagoj full_name: Fijan, Domagoj last_name: Fijan - first_name: Roger A. full_name: Lightwood, Roger A. last_name: Lightwood - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Christoph full_name: Dellago, Christoph last_name: Dellago - first_name: Daan full_name: Frenkel, Daan last_name: Frenkel citation: ama: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 2017;114(19):4911-4914. doi:10.1073/pnas.1621494114 apa: Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., & Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1621494114 chicago: Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621494114. ieee: P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel, “Numerical evidence for thermally induced monopoles,” Proceedings of the National Academy of Sciences, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914, 2017. ista: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 114(19), 4911–4914. mla: Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.” Proceedings of the National Academy of Sciences, vol. 114, no. 19, National Academy of Sciences, 2017, pp. 4911–14, doi:10.1073/pnas.1621494114. short: P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel, Proceedings of the National Academy of Sciences 114 (2017) 4911–4914. date_created: 2021-11-29T09:28:24Z date_published: 2017-04-24T00:00:00Z date_updated: 2021-11-29T09:59:12Z day: '24' doi: 10.1073/pnas.1621494114 extern: '1' external_id: arxiv: - '1610.06840' pmid: - '28439003' intvolume: ' 114' issue: '19' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.pnas.org/content/114/19/4911 month: '04' oa: 1 oa_version: Published Version page: 4911-4914 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Numerical evidence for thermally induced monopoles type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 114 year: '2017' ... --- _id: '10374' abstract: - lang: eng text: The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins. Here we show that this range of behaviour can be quantitatively captured by a single unifying Petri net that describes filamentous growth in terms of aggregate number and aggregate mass concentrations. By considering general features associated with a particular network connectivity, we are able to establish directly the rate-determining steps of the overall aggregation reaction from the system's scaling behaviour. We illustrate the power of this framework on a range of different experimental and simulated aggregating systems. The approach is general and will be applicable to any future extensions of the reaction network of filamentous self-assembly. acknowledgement: The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (SL, TPJK), Sidney Sussex College Cambridge (GM), the Frances and Augusta Newman Foundation (TPJK), the Biotechnology and Biological Science Research Council (TPJK), the Swedish Research Council (SL), the Academy of Medical Sciences (AŠ), Wellcome Trust (AŠ), and the Cambridge Centre for Misfolding Diseases (CMD, TPJK, MV). article_processing_charge: No article_type: original author: - first_name: Georg full_name: Meisl, Georg last_name: Meisl - first_name: Luke full_name: Rajah, Luke last_name: Rajah - first_name: Samuel A. I. full_name: Cohen, Samuel A. I. last_name: Cohen - first_name: Manuela full_name: Pfammatter, Manuela last_name: Pfammatter - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Erik full_name: Hellstrand, Erik last_name: Hellstrand - first_name: Alexander K. full_name: Buell, Alexander K. last_name: Buell - first_name: Adriano full_name: Aguzzi, Adriano last_name: Aguzzi - first_name: Sara full_name: Linse, Sara last_name: Linse - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles citation: ama: Meisl G, Rajah L, Cohen SAI, et al. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. 2017;8(10):7087-7097. doi:10.1039/c7sc01965c apa: Meisl, G., Rajah, L., Cohen, S. A. I., Pfammatter, M., Šarić, A., Hellstrand, E., … Knowles, T. P. J. (2017). Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c7sc01965c chicago: Meisl, Georg, Luke Rajah, Samuel A. I. Cohen, Manuela Pfammatter, Anđela Šarić, Erik Hellstrand, Alexander K. Buell, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” Chemical Science. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7sc01965c. ieee: G. Meisl et al., “Scaling behaviour and rate-determining steps in filamentous self-assembly,” Chemical Science, vol. 8, no. 10. Royal Society of Chemistry, pp. 7087–7097, 2017. ista: Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK, Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. 2017. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. 8(10), 7087–7097. mla: Meisl, Georg, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” Chemical Science, vol. 8, no. 10, Royal Society of Chemistry, 2017, pp. 7087–97, doi:10.1039/c7sc01965c. short: G. Meisl, L. Rajah, S.A.I. Cohen, M. Pfammatter, A. Šarić, E. Hellstrand, A.K. Buell, A. Aguzzi, S. Linse, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Chemical Science 8 (2017) 7087–7097. date_created: 2021-11-29T09:29:31Z date_published: 2017-08-31T00:00:00Z date_updated: 2021-11-29T10:00:00Z day: '31' ddc: - '540' doi: 10.1039/c7sc01965c extern: '1' external_id: pmid: - '29147538' intvolume: ' 8' issue: '10' keyword: - general chemistry language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ main_file_link: - open_access: '1' url: https://pubs.rsc.org/en/content/articlelanding/2017/SC/C7SC01965C month: '08' oa: 1 oa_version: Published Version page: 7087-7097 pmid: 1 publication: Chemical Science publication_identifier: eissn: - 2041-6539 issn: - 2041-6520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Scaling behaviour and rate-determining steps in filamentous self-assembly tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 8 year: '2017' ... --- _id: '10375' abstract: - lang: eng text: 'Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins influence the membrane shape, the membrane shape affects the interactions between the proteins. To study these membrane-mediated interactions on closed and anisotropically curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as a model system. We find that two particles on a closed system always attract each other, and tend to align with the direction of largest curvature. Multiple particles form arcs, or, at large enough numbers, a complete ring surrounding the vesicle in its equatorial plane. The resulting vesicle shape resembles a snowman. Our results indicate that these physical interactions on membranes with anisotropic shapes can be exploited by cells to drive macromolecules to preferred regions of cellular or intracellular membranes, and utilized to initiate dynamic processes such as cell division. The same principle could be used to find the midplane of an artificial vesicle, as a first step towards dividing it into two equal parts.' acknowledgement: This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program. article_processing_charge: No article_type: original author: - first_name: Afshin full_name: Vahid, Afshin last_name: Vahid - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Timon full_name: Idema, Timon last_name: Idema citation: ama: Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 2017;13(28):4924-4930. doi:10.1039/c7sm00433h apa: Vahid, A., Šarić, A., & Idema, T. (2017). Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c7sm00433h chicago: Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7sm00433h. ieee: A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation on fluid vesicles,” Soft Matter, vol. 13, no. 28. Royal Society of Chemistry, pp. 4924–4930, 2017. ista: Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 13(28), 4924–4930. mla: Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter, vol. 13, no. 28, Royal Society of Chemistry, 2017, pp. 4924–30, doi:10.1039/c7sm00433h. short: A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930. date_created: 2021-11-29T10:00:39Z date_published: 2017-06-15T00:00:00Z date_updated: 2021-11-29T10:33:36Z day: '15' doi: 10.1039/c7sm00433h extern: '1' external_id: arxiv: - '1703.00776' pmid: - '28677712' intvolume: ' 13' issue: '28' keyword: - condensed matter physics - general chemistry language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ main_file_link: - open_access: '1' url: https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H month: '06' oa: 1 oa_version: Published Version page: 4924-4930 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Curvature variation controls particle aggregation on fluid vesicles tmp: 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) short: CC BY (3.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 13 year: '2017' ... --- _id: '10418' abstract: - lang: eng text: We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates "almost surely". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. "super-martingales") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains. acknowledgement: "McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4." article_number: '33' article_processing_charge: No article_type: original author: - first_name: Annabelle full_name: Mciver, Annabelle last_name: Mciver - first_name: Carroll full_name: Morgan, Carroll last_name: Morgan - first_name: Benjamin Lucien full_name: Kaminski, Benjamin Lucien last_name: Kaminski - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen citation: ama: Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121 apa: 'Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121' chicago: Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121. ieee: A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017. ista: Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33. mla: Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121. short: A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017). conference: end_date: 2018-01-13 location: Los Angeles, CA, United States name: 'POPL: Programming Languages' start_date: 2018-01-07 date_created: 2021-12-05T23:01:49Z date_published: 2017-12-07T00:00:00Z date_updated: 2021-12-07T08:04:14Z day: '07' department: - _id: KrCh - _id: ToHe doi: 10.1145/3158121 external_id: arxiv: - '1711.03588' intvolume: ' 2' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/doi/10.1145/3158121 month: '12' oa: 1 oa_version: Published Version publication: Proceedings of the ACM on Programming Languages publication_identifier: eissn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: A new proof rule for almost-sure termination type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 2 year: '2017' ... --- _id: '10663' abstract: - lang: eng text: 'The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures.' alternative_title: - Graduate Dissertations and Theses at Illinois article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 citation: ama: Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017. apa: Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign. chicago: Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017. ieee: H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017. ista: Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign. mla: Polshyn, Hryhoriy. Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures. University of Illinois at Urbana-Champaign, 2017. short: H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017. date_created: 2022-01-25T14:54:14Z date_published: 2017-09-18T00:00:00Z date_updated: 2022-01-25T15:00:26Z day: '18' degree_awarded: PhD extern: '1' keyword: - physics - superconductivity - magnetic force microscopy - phase slips language: - iso: eng main_file_link: - open_access: '1' url: http://hdl.handle.net/2142/99178 month: '09' oa: 1 oa_version: Published Version page: '103' publication_status: published publisher: University of Illinois at Urbana-Champaign status: public supervisor: - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian title: Magnetic force microscopy studies of mesoscopic superconducting structures type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2017' ... --- _id: '10745' abstract: - lang: eng text: New ways to investigate and manipulate fluxoid and vortex states of mesoscopic superconducting structures are of great interest. The states with multiple vortices or winding numbers could be useful for the study of vortex interactions and interference effects, the braiding of Majorana bound states by winding vortices, and the development of novel superconducting devices. We demonstrate a methodology based on magnetic force microscopy that allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. By using micro-magnet as a source of inhomogeneous magnetic field, we can efficiently explore the configuration space of fluxoid states. Scanning over the structure reveals the energy crossing points of the lowest laying fluxoid states. This is due the strong interaction of cantilever with thermally activated fluxoid transitions at points of degeneracy. We show that measured patterns of fluxoid transitions allow to identify the states, investigate their energetics, and manipulate them. Further, we show that the dynamics of driven fluxoid transitions can be described by stochastic resonance model, which provides a unique way of measuring fluxoid transition rate and related energy barrier for chosen transitions even in complicated structures alternative_title: - Bulletin of the American Physical Society article_number: P39.00011 article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Tyler full_name: Naibert, Tyler last_name: Naibert - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian citation: ama: 'Polshyn H, Naibert T, Budakian R. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In: APS March Meeting 2017. Vol 62. American Physical Society; 2017.' apa: 'Polshyn, H., Naibert, T., & Budakian, R. (2017). Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In APS March Meeting 2017 (Vol. 62). New Orleans, LA, United States: American Physical Society.' chicago: Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In APS March Meeting 2017, Vol. 62. American Physical Society, 2017. ieee: H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in APS March Meeting 2017, New Orleans, LA, United States, 2017, vol. 62, no. 4. ista: 'Polshyn H, Naibert T, Budakian R. 2017. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. APS March Meeting 2017. APS: American Physical Society, Bulletin of the American Physical Society, vol. 62, P39.00011.' mla: Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” APS March Meeting 2017, vol. 62, no. 4, P39.00011, American Physical Society, 2017. short: H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017. conference: end_date: 2017-03-17 location: New Orleans, LA, United States name: 'APS: American Physical Society' start_date: 2017-03-13 date_created: 2022-02-08T09:49:17Z date_published: 2017-03-01T00:00:00Z date_updated: 2022-02-08T10:44:35Z day: '01' extern: '1' intvolume: ' 62' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR17/Session/P39.11 month: '03' oa: 1 oa_version: Published Version publication: APS March Meeting 2017 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: ' Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures' type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 62 year: '2017' ... --- _id: '1075' alternative_title: - American Studies in Austria author: - first_name: Bernhard full_name: Wenzl, Bernhard id: 479E9046-F248-11E8-B48F-1D18A9856A87 last_name: Wenzl citation: ama: 'Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; In: Parker J, Poole R, eds. Austria and America: 20th-Century Cross-Cultural Encounters. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80.' apa: 'Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; In J. Parker & R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters (Vol. 15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.' chicago: 'Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;” In Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.' ieee: 'B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;,” in Austria and America: 20th-Century Cross-Cultural Encounters, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.' ista: 'Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot; In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.' mla: 'Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;” Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.' short: 'B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.' date_created: 2018-12-11T11:50:00Z date_published: 2017-02-01T00:00:00Z date_updated: 2021-01-12T06:48:06Z day: '01' ddc: - '001' editor: - first_name: Joshua full_name: Parker, Joshua last_name: Parker - first_name: Ralph full_name: Poole, Ralph last_name: Poole extern: '1' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:08:06Z date_updated: 2018-12-12T10:08:06Z file_id: '4666' file_name: IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf file_size: 380624 relation: main_file file_date_updated: 2018-12-12T10:08:06Z has_accepted_license: '1' intvolume: ' 15' language: - iso: eng month: '02' oa: 1 oa_version: None page: 73 - 80 publication: 'Austria and America: 20th-Century Cross-Cultural Encounters' publication_identifier: isbn: - 978-3643908124 publication_status: published publisher: LIT Verlag Berlin-Münster-Wien-Zürich-London publist_id: '6306' status: public title: 'An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier"' type: book_chapter user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2017' ... --- _id: '11066' abstract: - lang: eng text: Recent studies have shown that a subset of nucleoporins (Nups) can detach from the nuclear pore complex and move into the nuclear interior to regulate transcription. One such dynamic Nup, called Nup98, has been implicated in gene activation in healthy cells and has been shown to drive leukemogenesis when mutated in patients with acute myeloid leukemia (AML). Here we show that in hematopoietic cells, Nup98 binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS (complex of proteins associated with Set1) complex, which is required for deposition of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark. Depletion of Nup98 or Wdr82 abolishes Set1A recruitment to chromatin and subsequently ablates H3K4me3 at adjacent promoters. Furthermore, expression of a Nup98 fusion protein implicated in aggressive AML causes mislocalization of H3K4me3 at abnormal regions and up-regulation of associated genes. Our findings establish a function of Nup98 in hematopoietic gene activation and provide mechanistic insight into which Nup98 leukemic fusion proteins promote AML. article_processing_charge: No article_type: original author: - first_name: Tobias M. full_name: Franks, Tobias M. last_name: Franks - first_name: Asako full_name: McCloskey, Asako last_name: McCloskey - first_name: Maxim Nikolaievich full_name: Shokhirev, Maxim Nikolaievich last_name: Shokhirev - first_name: Chris full_name: Benner, Chris last_name: Benner - first_name: Annie full_name: Rathore, Annie last_name: Rathore - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. 2017;31(22):2222-2234. doi:10.1101/gad.306753.117 apa: Franks, T. M., McCloskey, A., Shokhirev, M. N., Benner, C., Rathore, A., & Hetzer, M. (2017). Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.306753.117 chicago: Franks, Tobias M., Asako McCloskey, Maxim Nikolaievich Shokhirev, Chris Benner, Annie Rathore, and Martin Hetzer. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.” Genes & Development. Cold Spring Harbor Laboratory, 2017. https://doi.org/10.1101/gad.306753.117. ieee: T. M. Franks, A. McCloskey, M. N. Shokhirev, C. Benner, A. Rathore, and M. Hetzer, “Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells,” Genes & Development, vol. 31, no. 22. Cold Spring Harbor Laboratory, pp. 2222–2234, 2017. ista: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. 2017. Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. 31(22), 2222–2234. mla: Franks, Tobias M., et al. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.” Genes & Development, vol. 31, no. 22, Cold Spring Harbor Laboratory, 2017, pp. 2222–34, doi:10.1101/gad.306753.117. short: T.M. Franks, A. McCloskey, M.N. Shokhirev, C. Benner, A. Rathore, M. Hetzer, Genes & Development 31 (2017) 2222–2234. date_created: 2022-04-07T07:45:59Z date_published: 2017-12-21T00:00:00Z date_updated: 2022-07-18T08:33:05Z day: '21' doi: 10.1101/gad.306753.117 extern: '1' external_id: pmid: - '29269482' intvolume: ' 31' issue: '22' keyword: - Developmental Biology - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/gad.306753.117 month: '12' oa: 1 oa_version: Published Version page: 2222-2234 pmid: 1 publication: Genes & Development publication_identifier: issn: - 0890-9369 - 1549-5477 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 31 year: '2017' ... --- _id: '11067' abstract: - lang: eng text: Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that changes during differentiation. Nucleoporins are linked with cell-type-specific gene regulation, coupling physical changes in nuclear structure to transcriptional output; but, whether and how they coordinate with key fate-determining transcription factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2 in adult NeuPCs, where it is indispensable for their maintenance and controls neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional end sites correlates with increased or decreased gene expression, respectively, and inhibiting Nup153 expression alters open chromatin configurations at its target genes, disrupts genomic localization of Sox2, and promotes differentiation in vitro and a gliogenic fate switch in vivo. Together, these findings reveal that nuclear structural proteins may exert bimodal transcriptional effects to control cell fate. article_processing_charge: No article_type: original author: - first_name: Tomohisa full_name: Toda, Tomohisa last_name: Toda - first_name: Jonathan Y. full_name: Hsu, Jonathan Y. last_name: Hsu - first_name: Sara B. full_name: Linker, Sara B. last_name: Linker - first_name: Lauren full_name: Hu, Lauren last_name: Hu - first_name: Simon T. full_name: Schafer, Simon T. last_name: Schafer - first_name: Jerome full_name: Mertens, Jerome last_name: Mertens - first_name: Filipe V. full_name: Jacinto, Filipe V. last_name: Jacinto - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Fred H. full_name: Gage, Fred H. last_name: Gage citation: ama: Toda T, Hsu JY, Linker SB, et al. Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. 2017;21(5):618-634.e7. doi:10.1016/j.stem.2017.08.012 apa: Toda, T., Hsu, J. Y., Linker, S. B., Hu, L., Schafer, S. T., Mertens, J., … Gage, F. H. (2017). Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2017.08.012 chicago: Toda, Tomohisa, Jonathan Y. Hsu, Sara B. Linker, Lauren Hu, Simon T. Schafer, Jerome Mertens, Filipe V. Jacinto, Martin Hetzer, and Fred H. Gage. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells.” Cell Stem Cell. Elsevier, 2017. https://doi.org/10.1016/j.stem.2017.08.012. ieee: T. Toda et al., “Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells,” Cell Stem Cell, vol. 21, no. 5. Elsevier, p. 618–634.e7, 2017. ista: Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer M, Gage FH. 2017. Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. 21(5), 618–634.e7. mla: Toda, Tomohisa, et al. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells.” Cell Stem Cell, vol. 21, no. 5, Elsevier, 2017, p. 618–634.e7, doi:10.1016/j.stem.2017.08.012. short: T. Toda, J.Y. Hsu, S.B. Linker, L. Hu, S.T. Schafer, J. Mertens, F.V. Jacinto, M. Hetzer, F.H. Gage, Cell Stem Cell 21 (2017) 618–634.e7. date_created: 2022-04-07T07:46:12Z date_published: 2017-11-02T00:00:00Z date_updated: 2022-07-18T08:33:07Z day: '02' doi: 10.1016/j.stem.2017.08.012 extern: '1' external_id: pmid: - '28919367' intvolume: ' 21' issue: '5' keyword: - Cell Biology - Genetics - Molecular Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.stem.2017.08.012 month: '11' oa: 1 oa_version: Published Version page: 618-634.e7 pmid: 1 publication: Cell Stem Cell publication_identifier: issn: - 1934-5909 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 21 year: '2017' ... --- _id: '11065' abstract: - lang: eng text: Premature aging disorders provide an opportunity to study the mechanisms that drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins. We sought to investigate protein homeostasis in this disease. Here, we report a widespread increase in protein turnover in HGPS-derived cells compared to normal cells. We determine that global protein synthesis is elevated as a consequence of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts. Depleting normal lamin A or inducing mutant lamin A expression are each sufficient to drive nucleolar expansion. We further show that nucleolar size correlates with donor age in primary fibroblasts derived from healthy individuals and that ribosomal RNA production increases with age, indicating that nucleolar size and activity can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan in several systems, we show that increased ribosome biogenesis and activity are a hallmark of premature aging. article_number: '328' article_processing_charge: No article_type: original author: - first_name: Abigail full_name: Buchwalter, Abigail last_name: Buchwalter - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Buchwalter A, Hetzer M. Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. 2017;8. doi:10.1038/s41467-017-00322-z apa: Buchwalter, A., & Hetzer, M. (2017). Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-00322-z chicago: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein Translation in Premature Aging.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00322-z. ieee: A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017. ista: Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. 8, 328. mla: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein Translation in Premature Aging.” Nature Communications, vol. 8, 328, Springer Nature, 2017, doi:10.1038/s41467-017-00322-z. short: A. Buchwalter, M. Hetzer, Nature Communications 8 (2017). date_created: 2022-04-07T07:45:50Z date_published: 2017-08-30T00:00:00Z date_updated: 2022-07-18T08:33:03Z day: '30' doi: 10.1038/s41467-017-00322-z extern: '1' external_id: pmid: - '28855503' intvolume: ' 8' keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-017-00322-z month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Nucleolar expansion and elevated protein translation in premature aging type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 8 year: '2017' ... --- _id: '1112' abstract: - lang: eng text: There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes). author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Jorge full_name: Pérez Heredia, Jorge last_name: Pérez Heredia citation: ama: 'Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729' apa: 'Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729' chicago: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729. ieee: T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11. ista: 'Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.' mla: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729. short: T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11. conference: end_date: 2017-01-15 location: Copenhagen, Denmark name: 'FOGA: Foundations of Genetic Algorithms' start_date: 2017-01-12 date_created: 2018-12-11T11:50:12Z date_published: 2017-01-12T00:00:00Z date_updated: 2021-01-12T06:48:22Z day: '12' department: - _id: NiBa doi: 10.1145/3040718.3040729 language: - iso: eng month: '01' oa_version: None page: 3 - 11 publication: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms publication_identifier: isbn: - 978-145034651-1 publication_status: published publisher: ACM publist_id: '6255' quality_controlled: '1' scopus_import: 1 status: public title: An application of stochastic differential equations to evolutionary algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '11518' abstract: - lang: eng text: "We present spectroscopic follow-up observations of CR7 with ALMA, targeted at constraining the infrared (IR) continuum and [C II]158 mm line-emission at high spatial resolution matched to the HST/WFC3 imaging. CR7 is a luminous Lyα emitting galaxy at z = 6.6 that consists of three separated UV-continuum components. Our observations reveal several well-separated components of [C II] emission. The two most luminous components in [C II] coincide with the brightest UV components (A and B), blueshifted by »150 km s−1 with respect to the\r\npeak of Lyα emission. Other [C II] components are observed close to UV clumps B and C and are blueshifted by »300 and ≈80 km s−1 with respect to the systemic redshift. We do not detect FIR continuum emission due to dust with a 3σ limiting luminosity LIR T L d 35 K 3.1 10 = <´ 10 ( ) . This allows us to mitigate uncertainties in the dust-corrected SFR and derive SFRs for the three UV clumps A, B, and C of 28, 5, and 7 M yr−1. All clumps have [C II] luminosities consistent within the scatter observed in the local relation between SFR and L[ ] C II , implying that strong Lyα emission does not necessarily anti-correlate with [C II] luminosity. Combining\r\nour measurements with the literature, we show that galaxies with blue UV slopes have weaker [C II] emission at fixed SFR, potentially due to their lower metallicities and/or higher photoionization. Comparison with hydrodynamical simulations suggests that CR7ʼs clumps have metallicities of 0.1 Z Z 0.2 < < . The observed ISM structure of CR7 indicates that we are likely witnessing the build up of a central galaxy in the early universe through complex accretion of satellites." acknowledgement: 'We thank the referee for their constructive comments, which have helped improve the quality and clarity of this work. We thank Raffaella Schneider for comments on an earlier version of this paper. We thank Leindert Boogaard, Steven Bos, Rychard Bouwens, and Renske Smit for discussions. J.M. acknowledges the support of a Huygens PhD fellowship from Leiden University. D.S. acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. A.F. acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120. B.D. acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2015.1.00122.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ.' article_number: '145' article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: D. full_name: Sobral, D. last_name: Sobral - first_name: F. full_name: Boone, F. last_name: Boone - first_name: H. full_name: Röttgering, H. last_name: Röttgering - first_name: D. full_name: Schaerer, D. last_name: Schaerer - first_name: M. full_name: Girard, M. last_name: Girard - first_name: A. full_name: Pallottini, A. last_name: Pallottini - first_name: L. full_name: Vallini, L. last_name: Vallini - first_name: A. full_name: Ferrara, A. last_name: Ferrara - first_name: B. full_name: Darvish, B. last_name: Darvish - first_name: B. full_name: Mobasher, B. last_name: Mobasher citation: ama: Matthee JJ, Sobral D, Boone F, et al. ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. 2017;851(2). doi:10.3847/1538-4357/aa9931 apa: Matthee, J. J., Sobral, D., Boone, F., Röttgering, H., Schaerer, D., Girard, M., … Mobasher, B. (2017). ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/aa9931 chicago: Matthee, Jorryt J, D. Sobral, F. Boone, H. Röttgering, D. Schaerer, M. Girard, A. Pallottini, et al. “ALMA Reveals Metals yet No Dust within Multiple Components in CR7.” The Astrophysical Journal. IOP Publishing, 2017. https://doi.org/10.3847/1538-4357/aa9931. ieee: J. J. Matthee et al., “ALMA reveals metals yet no dust within multiple components in CR7,” The Astrophysical Journal, vol. 851, no. 2. IOP Publishing, 2017. ista: Matthee JJ, Sobral D, Boone F, Röttgering H, Schaerer D, Girard M, Pallottini A, Vallini L, Ferrara A, Darvish B, Mobasher B. 2017. ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. 851(2), 145. mla: Matthee, Jorryt J., et al. “ALMA Reveals Metals yet No Dust within Multiple Components in CR7.” The Astrophysical Journal, vol. 851, no. 2, 145, IOP Publishing, 2017, doi:10.3847/1538-4357/aa9931. short: J.J. Matthee, D. Sobral, F. Boone, H. Röttgering, D. Schaerer, M. Girard, A. Pallottini, L. Vallini, A. Ferrara, B. Darvish, B. Mobasher, The Astrophysical Journal 851 (2017). date_created: 2022-07-07T08:48:04Z date_published: 2017-12-21T00:00:00Z date_updated: 2022-08-18T10:23:35Z day: '21' doi: 10.3847/1538-4357/aa9931 extern: '1' external_id: arxiv: - '1709.06569' intvolume: ' 851' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - dark ages - reionization - 'first stars – galaxies: formation – galaxies: high-redshift – galaxies: ISM – galaxies: kinematics and dynamics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.06569 month: '12' oa: 1 oa_version: Preprint publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: ALMA reveals metals yet no dust within multiple components in CR7 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 851 year: '2017' ... --- _id: '11562' abstract: - lang: eng text: We present the CAlibrating LYMan-α with Hα (CALYMHA) pilot survey and new results on Lyman α (Lyα) selected galaxies at z ∼ 2. We use a custom-built Lyα narrow-band filter at the Isaac Newton Telescope, designed to provide a matched volume coverage to the z = 2.23 Hα HiZELS survey. Here, we present the first results for the COSMOS and UDS fields. Our survey currently reaches a 3σ line flux limit of ∼4 × 10−17 erg s−1 cm−2, and a Lyα luminosity limit of ∼1042.3 erg s−1. We find 188 Lyα emitters over 7.3 × 105 Mpc3, but also find significant numbers of other line-emitting sources corresponding to He II, C III] and C IV emission lines. These sources are important contaminants, and we carefully remove them, unlike most previous studies. We find that the Lyα luminosity function at z = 2.23 is very well described by a Schechter function up to LLy α ≈ 1043 erg s−1 with L∗=1042.59+0.16−0.08 erg s−1, ϕ∗=10−3.09+0.14−0.34 Mpc−3 and α = −1.75 ± 0.25. Above LLy α ≈ 1043 erg s−1, the Lyα luminosity function becomes power-law like, driven by X-ray AGN. We find that Lyα-selected emitters have a high escape fraction of 37 ± 7 per cent, anticorrelated with Lyα luminosity and correlated with Lyα equivalent width. Lyα emitters have ubiquitous large (≈40 kpc) Lyα haloes, ∼2 times larger than their Hα extents. By directly comparing our Lyα and Hα luminosity functions, we find that the global/overall escape fraction of Lyα photons (within a 13 kpc radius) from the full population of star-forming galaxies is 5.1 ± 0.2 per cent at the peak of the star formation history. An extra 3.3 ± 0.3 per cent of Lyα photons likely still escape, but at larger radii. acknowledgement: 'We thank the reviewer for his/her helpful comments and suggestions that have greatly improved this work. DS and JM acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. DS also acknowledges funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). PNB is grateful for support from the UK STFC via grant ST/M001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson merit award. We thank Matthew Hayes, Ryan Trainor, Kimihiko Nakajima and Anne Verhamme for many helpful discussions and Ana Sobral, Carolina Duarte and Miguel Domingos for taking part in observations with the NB392 filter. We also thank Sergio Santos for helpful comments. This research is based on observations obtained on the Isaac Newton Telescope (INT), programs: I13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B & I15AN008. The authors acknowledge the award of time from programmes: I13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B, I15AN008 on the INT. INT is operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 098.A 0819. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP (Bertin & Arnouts 1996; Bertin 2010), SCAMP (Bertin 2006) and TOPCAT (Taylor 2005). Dedicated to the memory of M. L. Nicolau and M. C. Serrano.' article_processing_charge: No article_type: original author: - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Philip full_name: Best, Philip last_name: Best - first_name: Andra full_name: Stroe, Andra last_name: Stroe - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Iván full_name: Oteo, Iván last_name: Oteo - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: Leah full_name: Morabito, Leah last_name: Morabito - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso citation: ama: 'Sobral D, Matthee JJ, Best P, et al. The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. 2017;466(1):1242-1258. doi:10.1093/mnras/stw3090' apa: 'Sobral, D., Matthee, J. J., Best, P., Stroe, A., Röttgering, H., Oteo, I., … Paulino-Afonso, A. (2017). The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw3090' chicago: 'Sobral, David, Jorryt J Matthee, Philip Best, Andra Stroe, Huub Röttgering, Iván Oteo, Ian Smail, Leah Morabito, and Ana Paulino-Afonso. “The CALYMHA Survey: Lyα Luminosity Function and Global Escape Fraction of Lyα Photons at z = 2.23.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw3090.' ieee: 'D. Sobral et al., “The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23,” Monthly Notices of the Royal Astronomical Society, vol. 466, no. 1. Oxford University Press, pp. 1242–1258, 2017.' ista: 'Sobral D, Matthee JJ, Best P, Stroe A, Röttgering H, Oteo I, Smail I, Morabito L, Paulino-Afonso A. 2017. The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. 466(1), 1242–1258.' mla: 'Sobral, David, et al. “The CALYMHA Survey: Lyα Luminosity Function and Global Escape Fraction of Lyα Photons at z = 2.23.” Monthly Notices of the Royal Astronomical Society, vol. 466, no. 1, Oxford University Press, 2017, pp. 1242–58, doi:10.1093/mnras/stw3090.' short: D. Sobral, J.J. Matthee, P. Best, A. Stroe, H. Röttgering, I. Oteo, I. Smail, L. Morabito, A. Paulino-Afonso, Monthly Notices of the Royal Astronomical Society 466 (2017) 1242–1258. date_created: 2022-07-12T12:04:16Z date_published: 2017-04-01T00:00:00Z date_updated: 2022-08-19T07:18:20Z day: '01' doi: 10.1093/mnras/stw3090 extern: '1' external_id: arxiv: - '1609.05897' intvolume: ' 466' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: haloes' - 'galaxies: high-redshift' - 'galaxies: luminosity function' - mass function - 'galaxies: statistics' - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.05897 month: '04' oa: 1 oa_version: Preprint page: 1242-1258 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 466 year: '2017' ... --- _id: '11566' abstract: - lang: eng text: While traditionally associated with active galactic nuclei (AGN), the properties of the C II] (λ = 2326 Å), C III] (λ, λ = 1907, 1909 Å) and C IV (λ, λ = 1549, 1551 Å) emission lines are still uncertain as large, unbiased samples of sources are scarce. We present the first blind, statistical study of C II], C III] and C IV emitters at z ∼ 0.68, 1.05, 1.53, respectively, uniformly selected down to a flux limit of ∼4 × 10−17 erg s−1 cm−1 through a narrow-band survey covering an area of ∼1.4 deg2 over COSMOS and UDS. We detect 16 C II], 35 C III] and 17 C IV emitters, whose nature we investigate using optical colours as well as Hubble Space Telescope (HST), X-ray, radio and far-infrared data. We find that z ∼ 0.7 C II] emitters are consistent with a mixture of blue (UV slope β = −2.0 ± 0.4) star-forming (SF) galaxies with discy HST structure and AGN with Seyfert-like morphologies. Bright C II] emitters have individual X-ray detections as well as high average black hole accretion rates (BHARs) of ∼0.1 M⊙ yr−1. C III] emitters at z ∼ 1.05 trace a general population of SF galaxies, with β = −0.8 ± 1.1, a variety of optical morphologies, including isolated and interacting galaxies and low BHAR (<0.02 M⊙ yr−1). Our C IV emitters at z ∼ 1.5 are consistent with young, blue quasars (β ∼ −1.9) with point-like optical morphologies, bright X-ray counterparts and large BHAR (0.8  M⊙ yr−1). We also find some surprising C II], C III] and C IV emitters with rest-frame equivalent widths (EWs) that could be as large as 50–100 Å. AGN or spatial offsets between the UV continuum stellar disc and the line-emitting regions may explain the large EW. These bright C II], C III] and C IV emitters are ideal candidates for spectroscopic follow-up to fully unveil their nature. acknowledgement: 'We would like to thank the anonymous referee for her/his valuable input that helped improve the clarity and interpretation of our results. DS acknowledges financial support from the Netherlands Organisation for Scientific research (NWO), through a Veni fellowship. IO acknowledges support from the European Research Council in the form of the Advanced Investigator Programme, 321302, COSMICISM. CALYMHA data are based on observations made with the Isaac Newton Telescope (proposals 13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B, I15AN008) operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias. Also based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 098.A-0819 and 179.A-2005. We are grateful to E. L. Wright and J. Schombert for their cosmology calculator. We would like to thank the authors of NUMPY (van der Walt et al. 2011), SCIPY (Jones et al. 2001), MATPLOTLIB (Hunter 2007) and ASTROPY (Astropy Collaboration et al. 2013) for making these packages publicly available. This research has made use of the NASA/IPAC Extragalactic Database (NED), which is ' article_processing_charge: No article_type: original author: - first_name: Andra full_name: Stroe, Andra last_name: Stroe - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: João full_name: Calhau, João last_name: Calhau - first_name: Ivan full_name: Oteo, Ivan last_name: Oteo citation: ama: Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. 2017;471(3):2558-2574. doi:10.1093/mnras/stx1712 apa: Stroe, A., Sobral, D., Matthee, J. J., Calhau, J., & Oteo, I. (2017). A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1712 chicago: Stroe, Andra, David Sobral, Jorryt J Matthee, João Calhau, and Ivan Oteo. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, Morphologies and Equivalent Widths .” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1712. ieee: A. Stroe, D. Sobral, J. J. Matthee, J. Calhau, and I. Oteo, “A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths ,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3. Oxford University Press, pp. 2558–2574, 2017. ista: Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. 2017. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. 471(3), 2558–2574. mla: Stroe, Andra, et al. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, Morphologies and Equivalent Widths .” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3, Oxford University Press, 2017, pp. 2558–74, doi:10.1093/mnras/stx1712. short: A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2558–2574. date_created: 2022-07-12T12:33:16Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-08-19T07:59:57Z day: '01' doi: 10.1093/mnras/stx1712 extern: '1' external_id: arxiv: - '1703.10169' intvolume: ' 471' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: active' - 'galaxies: high-redshift' - 'quasars: emission lines' - 'galaxies: star formation' - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.10169 month: '11' oa: 1 oa_version: Preprint page: 2558-2574 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11564' abstract: - lang: eng text: We study the production rate of ionizing photons of a sample of 588 Hα emitters (HAEs) and 160 Lyman-α emitters (LAEs) at z = 2.2 in the COSMOS field in order to assess the implied emissivity from galaxies, based on their ultraviolet (UV) luminosity. By exploring the rest-frame Lyman Continuum (LyC) with GALEX/NUV data, we find fesc < 2.8 (6.4) per cent through median (mean) stacking. By combining the Hα luminosity density with intergalactic medium emissivity measurements from absorption studies, we find a globally averaged 〈fesc〉 of 5.9+14.5−4.2 per cent at z = 2.2 if we assume HAEs are the only source of ionizing photons. We find similarly low values of the global 〈fesc〉 at z ≈ 3–5, also ruling out a high 〈fesc〉 at z < 5. These low escape fractions allow us to measure ξion, the number of produced ionizing photons per unit UV luminosity, and investigate how this depends on galaxy properties. We find a typical ξion ≈ 1024.77 ± 0.04 Hz erg−1 for HAEs and ξion ≈ 1025.14 ± 0.09 Hz erg−1 for LAEs. LAEs and low-mass HAEs at z = 2.2 show similar values of ξion as typically assumed in the reionization era, while the typical HAE is three times less ionizing. Due to an increasing ξion with increasing EW(Hα), ξion likely increases with redshift. This evolution alone is fully in line with the observed evolution of ξion between z ≈ 2 and 5, indicating a typical value of ξion ≈ 1025.4 Hz erg−1 in the reionization era. acknowledgement: "We thank the referee for the many helpful and constructive comments which have significantly improved this paper. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). PNB is grateful for support from the UK STFC via grant ST/M001229/1. IO acknowledges support from the European Research Council in the form of the Advanced Investigator Programme, 321302, COSMICISM. The authors thank Andreas Faisst, Michael Rutkowski and Andreas Sandberg for answering questions related to this work and Daniel Schaerer and Mark Dijkstra for discussions. We acknowledge the work that has been done by both the COSMOS team in assembling such large, state-of-the-art multi-wavelength data set, as this has been crucial for the results presented in this paper. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY (Jones et al. 2001; Hunter 2007; Van Der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration et al. 2013) packages, the astronomical imaging tools SEXTRACTOR and SWARP (Bertin & Arnouts 1996;\r\nBertin 2010) and the TOPCAT analysis program (Taylor 2013)." article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Philip full_name: Best, Philip last_name: Best - first_name: Ali Ahmad full_name: Khostovan, Ali Ahmad last_name: Khostovan - first_name: Iván full_name: Oteo, Iván last_name: Oteo - first_name: Rychard full_name: Bouwens, Rychard last_name: Bouwens - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering citation: ama: Matthee JJ, Sobral D, Best P, et al. The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. 2017;465(3):3637-3655. doi:10.1093/mnras/stw2973 apa: Matthee, J. J., Sobral, D., Best, P., Khostovan, A. A., Oteo, I., Bouwens, R., & Röttgering, H. (2017). The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2973 chicago: Matthee, Jorryt J, David Sobral, Philip Best, Ali Ahmad Khostovan, Iván Oteo, Rychard Bouwens, and Huub Röttgering. “The Production and Escape of Lyman-Continuum Radiation from Star-Forming Galaxies at z ∼ 2 and Their Redshift Evolution.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2973. ieee: J. J. Matthee et al., “The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 3. Oxford University Press, pp. 3637–3655, 2017. ista: Matthee JJ, Sobral D, Best P, Khostovan AA, Oteo I, Bouwens R, Röttgering H. 2017. The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. 465(3), 3637–3655. mla: Matthee, Jorryt J., et al. “The Production and Escape of Lyman-Continuum Radiation from Star-Forming Galaxies at z ∼ 2 and Their Redshift Evolution.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 3, Oxford University Press, 2017, pp. 3637–55, doi:10.1093/mnras/stw2973. short: J.J. Matthee, D. Sobral, P. Best, A.A. Khostovan, I. Oteo, R. Bouwens, H. Röttgering, Monthly Notices of the Royal Astronomical Society 465 (2017) 3637–3655. date_created: 2022-07-12T12:12:14Z date_published: 2017-03-01T00:00:00Z date_updated: 2022-08-19T07:53:04Z day: '01' doi: 10.1093/mnras/stw2973 extern: '1' external_id: arxiv: - '1605.08782' intvolume: ' 465' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - 'cosmology: observations' - dark ages - reionization - first stars language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1605.08782 month: '03' oa: 1 oa_version: Preprint page: 3637-3655 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 465 year: '2017' ... --- _id: '11567' abstract: - lang: eng text: Recently, the C III] and C IV emission lines have been observed in galaxies in the early Universe (z > 5), providing new ways to measure their redshift and study their stellar populations and active galactic nuclei (AGN). We explore the first blind C II], C III] and C IV survey (z ∼ 0.68, 1.05, 1.53, respectively) presented in Stroe et al. (2017). We derive luminosity functions (LF) and study properties of C II], C III] and C IV line emitters through comparisons to the LFs of H α and Ly α emitters, UV selected star-forming (SF) galaxies and quasars at similar redshifts. The C II] LF at z ∼ 0.68 is equally well described by a Schechter or a power-law LF, characteristic of a mixture of SF and AGN activity. The C III] LF (z ∼ 1.05) is consistent to a scaled down version of the Schechter H α and Ly α LF at their redshift, indicating a SF origin. In stark contrast, the C IV LF at z ∼ 1.53 is well fit by a power-law, quasar-like LF. We find that the brightest UV sources (MUV < −22) will universally have C III] and C IV emission. However, on average, C III] and C IV are not as abundant as H α or Ly α emitters at the same redshift, with cosmic average ratios of ∼0.02–0.06 to H α and ∼0.01–0.1 to intrinsic Ly α. We predict that the C III] and C IV lines can only be truly competitive in confirming high-redshift candidates when the hosts are intrinsically bright and the effective Ly α escape fraction is below 1 per cent. While C III] and C IV were proposed as good tracers of young, relatively low-metallicity galaxies typical of the early Universe, we find that, at least at z ∼ 1.5, C IV is exclusively hosted by AGN/quasars, especially at large line equivalent widths. article_processing_charge: No article_type: original author: - first_name: Andra full_name: Stroe, Andra last_name: Stroe - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: João full_name: Calhau, João last_name: Calhau - first_name: Ivan full_name: Oteo, Ivan last_name: Oteo citation: ama: Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. 2017;471(3):2575-2586. doi:10.1093/mnras/stx1713 apa: Stroe, A., Sobral, D., Matthee, J. J., Calhau, J., & Oteo, I. (2017). A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1713 chicago: Stroe, Andra, David Sobral, Jorryt J Matthee, João Calhau, and Ivan Oteo. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity Functions and Cosmic Average Line Ratios.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1713. ieee: A. Stroe, D. Sobral, J. J. Matthee, J. Calhau, and I. Oteo, “A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3. Oxford University Press, pp. 2575–2586, 2017. ista: Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. 2017. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. 471(3), 2575–2586. mla: Stroe, Andra, et al. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity Functions and Cosmic Average Line Ratios.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3, Oxford University Press, 2017, pp. 2575–86, doi:10.1093/mnras/stx1713. short: A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2575–2586. date_created: 2022-07-12T12:54:57Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-08-19T08:02:04Z day: '01' doi: 10.1093/mnras/stx1713 extern: '1' external_id: arxiv: - '1703.10169' intvolume: ' 471' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: active' - 'galaxies: high redshift' - 'galaxies: luminosity function' - mass function - 'quasars: emission lines' - star formation - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.10169 month: '11' oa: 1 oa_version: Preprint page: 2575-2586 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11565' abstract: - lang: eng text: We use the hydrodynamical EAGLE simulation to study the magnitude and origin of the scatter in the stellar mass–halo mass relation for central galaxies. We separate cause and effect by correlating stellar masses in the baryonic simulation with halo properties in a matched dark matter only (DMO) simulation. The scatter in stellar mass increases with redshift and decreases with halo mass. At z = 0.1, it declines from 0.25 dex at M200, DMO ≈ 1011 M⊙ to 0.12 dex at M200, DMO ≈ 1013 M⊙, but the trend is weak above 1012 M⊙. For M200, DMO < 1012.5 M⊙ up to 0.04 dex of the scatter is due to scatter in the halo concentration. At fixed halo mass, a larger stellar mass corresponds to a more concentrated halo. This is likely because higher concentrations imply earlier formation times and hence more time for accretion and star formation, and/or because feedback is less efficient in haloes with higher binding energies. The maximum circular velocity, Vmax, DMO, and binding energy are therefore more fundamental properties than halo mass, meaning that they are more accurate predictors of stellar mass, and we provide fitting formulae for their relations with stellar mass. However, concentration alone cannot explain the total scatter in the Mstar−M200,DMO relation, and it does not explain the scatter in Mstar–Vmax, DMO. Halo spin, sphericity, triaxiality, substructure and environment are also not responsible for the remaining scatter, which thus could be due to more complex halo properties or non-linear/stochastic baryonic effects. acknowledgement: We thank the anonymous referee for their comments. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. JM thanks David Sobral for useful discussions and help with fitting routines and Jonas Chavez Montero and Ying Zu for providing data. We thank PRACE for the access to the Curie facility in France. We have used the DiRAC system which is a part of National E-Infrastructure at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk); the equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, STFC DiRAC Operations grant ST/K003267/1 and Durham University. The study was sponsored by the Dutch National Computing Facilities Foundation (NCF) for the use of supercomputer facilities, with financial support from the Netherlands Organisation for Scientific Research (NWO), through VICI grant 639.043.409, and the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement 278594- GasAroundGalaxies, and from the Belgian Science Policy Office ([AP P7/08 CHARM]). We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY, H5PY and RPY2 packages, and the TOPCAT analysis program (Taylor 2005). article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Joop full_name: Schaye, Joop last_name: Schaye - first_name: Robert A. full_name: Crain, Robert A. last_name: Crain - first_name: Matthieu full_name: Schaller, Matthieu last_name: Schaller - first_name: Richard full_name: Bower, Richard last_name: Bower - first_name: Tom full_name: Theuns, Tom last_name: Theuns citation: ama: Matthee JJ, Schaye J, Crain RA, Schaller M, Bower R, Theuns T. The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. 2017;465(2):2381-2396. doi:10.1093/mnras/stw2884 apa: Matthee, J. J., Schaye, J., Crain, R. A., Schaller, M., Bower, R., & Theuns, T. (2017). The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2884 chicago: Matthee, Jorryt J, Joop Schaye, Robert A. Crain, Matthieu Schaller, Richard Bower, and Tom Theuns. “The Origin of Scatter in the Stellar Mass–Halo Mass Relation of Central Galaxies in the EAGLE Simulation.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2884. ieee: J. J. Matthee, J. Schaye, R. A. Crain, M. Schaller, R. Bower, and T. Theuns, “The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 2. Oxford University Press, pp. 2381–2396, 2017. ista: Matthee JJ, Schaye J, Crain RA, Schaller M, Bower R, Theuns T. 2017. The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. 465(2), 2381–2396. mla: Matthee, Jorryt J., et al. “The Origin of Scatter in the Stellar Mass–Halo Mass Relation of Central Galaxies in the EAGLE Simulation.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 2, Oxford University Press, 2017, pp. 2381–96, doi:10.1093/mnras/stw2884. short: J.J. Matthee, J. Schaye, R.A. Crain, M. Schaller, R. Bower, T. Theuns, Monthly Notices of the Royal Astronomical Society 465 (2017) 2381–2396. date_created: 2022-07-12T12:25:08Z date_published: 2017-02-01T00:00:00Z date_updated: 2022-08-19T07:56:07Z day: '01' doi: 10.1093/mnras/stw2884 extern: '1' external_id: arxiv: - '1608.08218' intvolume: ' 465' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: formation' - 'galaxies: haloes' - 'cosmology: theory' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.08218 month: '02' oa: 1 oa_version: Preprint page: 2381-2396 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 465 year: '2017' ... --- _id: '11561' abstract: - lang: eng text: We present a sample of ∼1000 emission-line galaxies at z = 0.4–4.7 from the ∼0.7deg2 High-z Emission-Line Survey in the Boötes field identified with a suite of six narrow-band filters at ≈0.4–2.1 μm. These galaxies have been selected on their Ly α (73), [O II] (285), H β/[O III] (387) or H α (362) emission line, and have been classified with optical to near-infrared colours. A subsample of 98 sources have reliable redshifts from multiple narrow-band (e.g. [O II]–H α) detections and/or spectroscopy. In this survey paper, we present the observations, selection and catalogues of emitters. We measure number densities of Ly α, [O II], H β/[O III] and H α and confirm strong luminosity evolution in star-forming galaxies from z ∼ 0.4 to ∼5, in agreement with previous results. To demonstrate the usefulness of dual-line emitters, we use the sample of dual [O II]–H α emitters to measure the observed [O II]/H α ratio at z = 1.47. The observed [O II]/H α ratio increases significantly from 0.40 ± 0.01 at z = 0.1 to 0.52 ± 0.05 at z = 1.47, which we attribute to either decreasing dust attenuation with redshift, or due to a bias in the (typically) fibre measurements in the local Universe that only measure the central kpc regions. At the bright end, we find that both the H α and Ly α number densities at z ≈ 2.2 deviate significantly from a Schechter form, following a power law. We show that this is driven entirely by an increasing X-ray/active galactic nucleus fraction with line luminosity, which reaches ≈100 per cent at line luminosities L ≳ 3 × 1044 erg s−1. article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Philip full_name: Best, Philip last_name: Best - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: Fuyan full_name: Bian, Fuyan last_name: Bian - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Xiaohui full_name: Fan, Xiaohui last_name: Fan citation: ama: 'Matthee JJ, Sobral D, Best P, et al. Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. 2017;471(1):629-649. doi:10.1093/mnras/stx1569' apa: 'Matthee, J. J., Sobral, D., Best, P., Smail, I., Bian, F., Darvish, B., … Fan, X. (2017). Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1569' chicago: 'Matthee, Jorryt J, David Sobral, Philip Best, Ian Smail, Fuyan Bian, Behnam Darvish, Huub Röttgering, and Xiaohui Fan. “Boötes-HiZELS: An Optical to near-Infrared Survey of Emission-Line Galaxies at z = 0.4–4.7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1569.' ieee: 'J. J. Matthee et al., “Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 1. Oxford University Press, pp. 629–649, 2017.' ista: 'Matthee JJ, Sobral D, Best P, Smail I, Bian F, Darvish B, Röttgering H, Fan X. 2017. Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. 471(1), 629–649.' mla: 'Matthee, Jorryt J., et al. “Boötes-HiZELS: An Optical to near-Infrared Survey of Emission-Line Galaxies at z = 0.4–4.7.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 1, Oxford University Press, 2017, pp. 629–49, doi:10.1093/mnras/stx1569.' short: J.J. Matthee, D. Sobral, P. Best, I. Smail, F. Bian, B. Darvish, H. Röttgering, X. Fan, Monthly Notices of the Royal Astronomical Society 471 (2017) 629–649. date_created: 2022-07-12T11:01:35Z date_published: 2017-10-01T00:00:00Z date_updated: 2022-08-19T07:15:14Z day: '01' doi: 10.1093/mnras/stx1569 extern: '1' external_id: arxiv: - '1702.04721' intvolume: ' 471' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics galaxies - active - galaxies - evolution - galaxies - high-redshift - galaxies - luminosity function - mass function - 'galaxies: star formation' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.04721 month: '10' oa: 1 oa_version: Preprint page: 629-649 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11572' abstract: - lang: eng text: We present spectroscopic follow-up of candidate luminous Ly α emitters (LAEs) at z = 5.7–6.6 in the SA22 field with VLT/X-SHOOTER. We confirm two new luminous LAEs at z = 5.676 (SR6) and z = 6.532 (VR7), and also present HST follow-up of both sources. These sources have luminosities LLy α ≈ 3 × 1043 erg s−1, very high rest-frame equivalent widths of EW0 ≳ 200 Å and narrow Ly α lines (200–340 km s−1). VR7 is the most UV-luminous LAE at z > 6.5, with M1500 = −22.5, even brighter in the UV than CR7. Besides Ly α, we do not detect any other rest-frame UV lines in the spectra of SR6 and VR7, and argue that rest-frame UV lines are easier to observe in bright galaxies with low Ly α equivalent widths. We confirm that Ly α line widths increase with Ly α luminosity at z = 5.7, while there are indications that Ly α lines of faint LAEs become broader at z = 6.6, potentially due to reionization. We find a large spread of up to 3 dex in UV luminosity for >L⋆ LAEs, but find that the Ly α luminosity of the brightest LAEs is strongly related to UV luminosity at z = 6.6. Under basic assumptions, we find that several LAEs at z ≈ 6–7 have Ly α escape fractions ≳ 100  per cent, indicating bursty star formation histories, alternative Ly α production mechanisms, or dust attenuating Ly α emission differently than UV emission. Finally, we present a method to compute ξion, the production efficiency of ionizing photons, and find that LAEs at z ≈ 6–7 have high values of log10(ξion/Hz erg−1) ≈ 25.51 ± 0.09 that may alleviate the need for high Lyman-Continuum escape fractions required for reionization. acknowledgement: 'We thank the referee for a constructive report that has improved the quality and clarity of this work. The authors thank Grecco Oyarzún for discussions. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G. We thank Kasper Schmidt for providing measurements. Based on observations with the W.M. Keck Observatory through programme C267D. The W.M. Keck Observatory is operated as a scientific partnership amongst the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 097.A-0943, 294.A 5018 and 098.A-0819 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. The authors acknowledge the award of observing time (W16AN004) and of service time (SW2014b20) on the William Herschel Telescope (WHT). WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. Based on observations made with the NASA/ESA HST, obtained (from the Data Archive) at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with programme #14699. We are grateful for the excellent data sets from the COSMOS, UltraVISTA, SXDS, UDS and CFHTLS survey teams; without these legacy surveys, this research would have been impossible. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP and SCAMP and the TOPCAT analysis tool (Taylor 2013).' article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos - first_name: Bahram full_name: Mobasher, Bahram last_name: Mobasher - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Lara full_name: Alegre, Lara last_name: Alegre citation: ama: Matthee JJ, Sobral D, Darvish B, et al. Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. 2017;472(1):772-787. doi:10.1093/mnras/stx2061 apa: Matthee, J. J., Sobral, D., Darvish, B., Santos, S., Mobasher, B., Paulino-Afonso, A., … Alegre, L. (2017). Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx2061 chicago: Matthee, Jorryt J, David Sobral, Behnam Darvish, Sérgio Santos, Bahram Mobasher, Ana Paulino-Afonso, Huub Röttgering, and Lara Alegre. “Spectroscopic Properties of Luminous Ly α Emitters at z ≈ 6–7 and Comparison to the Lyman-Break Population.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx2061. ieee: J. J. Matthee et al., “Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population,” Monthly Notices of the Royal Astronomical Society, vol. 472, no. 1. Oxford University Press, pp. 772–787, 2017. ista: Matthee JJ, Sobral D, Darvish B, Santos S, Mobasher B, Paulino-Afonso A, Röttgering H, Alegre L. 2017. Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. 472(1), 772–787. mla: Matthee, Jorryt J., et al. “Spectroscopic Properties of Luminous Ly α Emitters at z ≈ 6–7 and Comparison to the Lyman-Break Population.” Monthly Notices of the Royal Astronomical Society, vol. 472, no. 1, Oxford University Press, 2017, pp. 772–87, doi:10.1093/mnras/stx2061. short: J.J. Matthee, D. Sobral, B. Darvish, S. Santos, B. Mobasher, A. Paulino-Afonso, H. Röttgering, L. Alegre, Monthly Notices of the Royal Astronomical Society 472 (2017) 772–787. date_created: 2022-07-13T09:47:39Z date_published: 2017-11-01T00:00:00Z date_updated: 2022-08-19T08:05:37Z day: '01' doi: 10.1093/mnras/stx2061 extern: '1' external_id: arxiv: - '1706.06591' intvolume: ' 472' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution – galaxies: high-redshift' - dark ages - reionization - first stars - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.06591 month: '11' oa: 1 oa_version: Preprint page: 772-787 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 472 year: '2017' ... --- _id: '11573' abstract: - lang: eng text: We present dynamical measurements from the KMOS (K-band multi-object spectrograph) Deep Survey (KDS), which comprises 77 typical star-forming galaxies at z ≃ 3.5 in the mass range 9.0 < log (M⋆/M⊙) < 10.5. These measurements constrain the internal dynamics, the intrinsic velocity dispersions (σint) and rotation velocities (VC) of galaxies in the high-redshift Universe. The mean velocity dispersion of the galaxies in our sample is σint=70.8+3.3−3.1kms−1⁠, revealing that the increasing average σint with increasing redshift, reported for z ≲ 2, continues out to z ≃ 3.5. Only 36 ± 8 per cent of our galaxies are rotation-dominated (VC/σint > 1), with the sample average VC/σint value much smaller than at lower redshift. After carefully selecting comparable star-forming samples at multiple epochs, we find that the rotation-dominated fraction evolves with redshift with a z−0.2 dependence. The rotation-dominated KDS galaxies show no clear offset from the local rotation velocity–stellar mass (i.e. VC–M⋆) relation, although a smaller fraction of the galaxies are on the relation due to the increase in the dispersion-dominated fraction. These observations are consistent with a simple equilibrium model picture, in which random motions are boosted in high-redshift galaxies by a combination of the increasing gas fractions, accretion efficiency, specific star formation rate and stellar feedback and which may provide significant pressure support against gravity on the galactic disc scale. acknowledgement: 'We wish to thank the anonymous referee for their comments, which have improved the quality and clarity of this work. OJT acknowledges the financial support of the Science and Technology Facilities Council through a studentship award. MC and OJT acknowledge the KMOS team and all the personnel of the European Southern Observatory Very Large Telescope for outstanding support during the KMOS GTO observations. CMH, AMS and RMS acknowledge the Science and Technology Facilities Council through grant code ST/L00075X/1. RJM acknowledges the support of the European Research Council via the award of a Consolidator Grant (PI: McLure). JSD acknowledges the support of the European Research Council via the award of an Advanced Grant (PI J. Dunlop), and the contribution of the EC FP7 SPACE project ASTRODEEP (Ref.No: 312725). AMS acknowledges the Leverhulme Foundation. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). This work is based on observations taken by the CANDELS Multi-Cycle Treasury Program with the NASA/ESA HST, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. This work is based on observations taken by the 3D HST Treasury Program (GO 12177 and 12328) with the NASA/ESA HST, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Based on data obtained with the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Program 185.A-0791, and made available by the VUDS team at the CESAM data centre, Laboratoire d’Astrophysique de Marseille, France. Based on observations obtained at the Very Large Telescope of the European Southern Observatory. Programme IDs: 092.A 0399(A), 093.A-0122(A,B), 094.A-0214(A,B),095.A0680(A,B),096.A-0315(A,B,C).' article_processing_charge: No article_type: original author: - first_name: O. J. full_name: Turner, O. J. last_name: Turner - first_name: M. full_name: Cirasuolo, M. last_name: Cirasuolo - first_name: C. M. full_name: Harrison, C. M. last_name: Harrison - first_name: R. J. full_name: McLure, R. J. last_name: McLure - first_name: J. S. full_name: Dunlop, J. S. last_name: Dunlop - first_name: A. M. full_name: Swinbank, A. M. last_name: Swinbank - first_name: H. L. full_name: Johnson, H. L. last_name: Johnson - first_name: D. full_name: Sobral, D. last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: R. M. full_name: Sharples, R. M. last_name: Sharples citation: ama: Turner OJ, Cirasuolo M, Harrison CM, et al. The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. 2017;471(2):1280-1320. doi:10.1093/mnras/stx1366 apa: Turner, O. J., Cirasuolo, M., Harrison, C. M., McLure, R. J., Dunlop, J. S., Swinbank, A. M., … Sharples, R. M. (2017). The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1366 chicago: Turner, O. J., M. Cirasuolo, C. M. Harrison, R. J. McLure, J. S. Dunlop, A. M. Swinbank, H. L. Johnson, D. Sobral, Jorryt J Matthee, and R. M. Sharples. “The KMOS Deep Survey (KDS) – I. Dynamical Measurements of Typical Star-Forming Galaxies at z ≃ 3.5.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1366. ieee: O. J. Turner et al., “The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 2. Oxford University Press, pp. 1280–1320, 2017. ista: Turner OJ, Cirasuolo M, Harrison CM, McLure RJ, Dunlop JS, Swinbank AM, Johnson HL, Sobral D, Matthee JJ, Sharples RM. 2017. The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. 471(2), 1280–1320. mla: Turner, O. J., et al. “The KMOS Deep Survey (KDS) – I. Dynamical Measurements of Typical Star-Forming Galaxies at z ≃ 3.5.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 2, Oxford University Press, 2017, pp. 1280–320, doi:10.1093/mnras/stx1366. short: O.J. Turner, M. Cirasuolo, C.M. Harrison, R.J. McLure, J.S. Dunlop, A.M. Swinbank, H.L. Johnson, D. Sobral, J.J. Matthee, R.M. Sharples, Monthly Notices of the Royal Astronomical Society 471 (2017) 1280–1320. date_created: 2022-07-13T10:03:01Z date_published: 2017-10-01T00:00:00Z date_updated: 2022-08-19T08:07:31Z day: '01' doi: 10.1093/mnras/stx1366 extern: '1' external_id: arxiv: - '1704.06263' intvolume: ' 471' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - 'galaxies: kinematics and dynamics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.06263 month: '10' oa: 1 oa_version: Preprint page: 1280-1320 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2017' ... --- _id: '11633' abstract: - lang: eng text: Our understanding of stars through asteroseismic data analysis is limited by our ability to take advantage of the huge amount of observed stars provided by space missions such as CoRoT, Kepler , K2, and soon TESS and PLATO. Global seismic pipelines provide global stellar parameters such as mass and radius using the mean seismic parameters, as well as the effective temperature. These pipelines are commonly used automatically on thousands of stars observed by K2 for 3 months (and soon TESS for at least ∼ 1 month). However, pipelines are not immune from misidentifying noise peaks and stellar oscillations. Therefore, new validation techniques are required to assess the quality of these results. We present a new metric called FliPer (Flicker in Power), which takes into account the average variability at all measured time scales. The proper calibration of FliPer enables us to obtain good estimations of global stellar parameters such as surface gravity that are robust against the influence of noise peaks and hence are an excellent way to find faults in asteroseismic pipelines. article_number: '1711.02890' article_processing_charge: No author: - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: R. A. full_name: Garcia, R. A. last_name: Garcia - first_name: G. R. full_name: Davies, G. R. last_name: Davies - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: E. full_name: Corsaro, E. last_name: Corsaro citation: ama: 'Bugnet LA, Garcia RA, Davies GR, Mathur S, Corsaro E. FliPer: Checking the reliability of global seismic parameters from automatic pipelines. arXiv. doi:10.48550/arXiv.1711.02890' apa: 'Bugnet, L. A., Garcia, R. A., Davies, G. R., Mathur, S., & Corsaro, E. (n.d.). FliPer: Checking the reliability of global seismic parameters from automatic pipelines. arXiv. https://doi.org/10.48550/arXiv.1711.02890' chicago: 'Bugnet, Lisa Annabelle, R. A. Garcia, G. R. Davies, S. Mathur, and E. Corsaro. “FliPer: Checking the Reliability of Global Seismic Parameters from Automatic Pipelines.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1711.02890.' ieee: 'L. A. Bugnet, R. A. Garcia, G. R. Davies, S. Mathur, and E. Corsaro, “FliPer: Checking the reliability of global seismic parameters from automatic pipelines,” arXiv. .' ista: 'Bugnet LA, Garcia RA, Davies GR, Mathur S, Corsaro E. FliPer: Checking the reliability of global seismic parameters from automatic pipelines. arXiv, 1711.02890.' mla: 'Bugnet, Lisa Annabelle, et al. “FliPer: Checking the Reliability of Global Seismic Parameters from Automatic Pipelines.” ArXiv, 1711.02890, doi:10.48550/arXiv.1711.02890.' short: L.A. Bugnet, R.A. Garcia, G.R. Davies, S. Mathur, E. Corsaro, ArXiv (n.d.). date_created: 2022-07-21T07:13:13Z date_published: 2017-11-08T00:00:00Z date_updated: 2022-08-22T08:45:42Z day: '08' doi: 10.48550/arXiv.1711.02890 extern: '1' external_id: arxiv: - '1711.02890' keyword: - asteroseismology - methods - data analysis - stars - oscillations language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1711.02890 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'FliPer: Checking the reliability of global seismic parameters from automatic pipelines' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '11651' abstract: - lang: eng text: Diffusions and related random walk procedures are of central importance in many areas of machine learning, data analysis, and applied mathematics. Because they spread mass agnostically at each step in an iterative manner, they can sometimes spread mass “too aggressively,” thereby failing to find the “right” clusters. We introduce a novel Capacity Releasing Diffusion (CRD) Process, which is both faster and stays more local than the classical spectral diffusion process. As an application, we use our CRD Process to develop an improved local algorithm for graph clustering. Our local graph clustering method can find local clusters in a model of clustering where one begins the CRD Process in a cluster whose vertices are connected better internally than externally by an O(log2n) factor, where n is the number of nodes in the cluster. Thus, our CRD Process is the first local graph clustering algorithm that is not subject to the well-known quadratic Cheeger barrier. Our result requires a certain smoothness condition, which we expect to be an artifact of our analysis. Our empirical evaluation demonstrates improved results, in particular for realistic social graphs where there are moderately good—but not very good—clusters. alternative_title: - PMLR article_processing_charge: No author: - first_name: Di full_name: Wang, Di last_name: Wang - first_name: Kimon full_name: Fountoulakis, Kimon last_name: Fountoulakis - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Michael W. full_name: Mahoney, Michael W. last_name: Mahoney - first_name: ' Satish' full_name: Rao , Satish last_name: 'Rao ' citation: ama: 'Wang D, Fountoulakis K, Henzinger MH, Mahoney MW, Rao Satish. Capacity releasing diffusion for speed and locality. In: Proceedings of the 34th International Conference on Machine Learning. Vol 70. ML Research Press; 2017:3598-3607.' apa: 'Wang, D., Fountoulakis, K., Henzinger, M. H., Mahoney, M. W., & Rao , Satish. (2017). Capacity releasing diffusion for speed and locality. In Proceedings of the 34th International Conference on Machine Learning (Vol. 70, pp. 3598–3607). Sydney, Australia: ML Research Press.' chicago: Wang, Di, Kimon Fountoulakis, Monika H Henzinger, Michael W. Mahoney, and Satish Rao . “Capacity Releasing Diffusion for Speed and Locality.” In Proceedings of the 34th International Conference on Machine Learning, 70:3598–3607. ML Research Press, 2017. ieee: D. Wang, K. Fountoulakis, M. H. Henzinger, M. W. Mahoney, and Satish Rao , “Capacity releasing diffusion for speed and locality,” in Proceedings of the 34th International Conference on Machine Learning, Sydney, Australia, 2017, vol. 70, pp. 3598–3607. ista: Wang D, Fountoulakis K, Henzinger MH, Mahoney MW, Rao Satish. 2017. Capacity releasing diffusion for speed and locality. Proceedings of the 34th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 70, 3598–3607. mla: Wang, Di, et al. “Capacity Releasing Diffusion for Speed and Locality.” Proceedings of the 34th International Conference on Machine Learning, vol. 70, ML Research Press, 2017, pp. 3598–607. short: D. Wang, K. Fountoulakis, M.H. Henzinger, M.W. Mahoney, Satish Rao , in:, Proceedings of the 34th International Conference on Machine Learning, ML Research Press, 2017, pp. 3598–3607. conference: end_date: 2017-08-11 location: Sydney, Australia name: International Conference on Machine Learning start_date: 2017-08-06 date_created: 2022-07-25T13:59:21Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-09T09:15:31Z day: '01' extern: '1' external_id: arxiv: - '1706.05826' intvolume: ' 70' language: - iso: eng main_file_link: - open_access: '1' url: http://proceedings.mlr.press/v70/wang17b/wang17b.pdf month: '09' oa: 1 oa_version: Published Version page: 3598-3607 publication: Proceedings of the 34th International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: Capacity releasing diffusion for speed and locality type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '11665' 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 present deterministic (1+ϵ)-approximation algorithms whose amortized time (over some number of link changes) is sublinear in D, the maximum diameter of the network.\r\n\r\nOur technique also leads to a deterministic (1+ϵ)-approximate incremental algorithm for single-source shortest paths in the sequential (usual RAM) model. Prior to our work, the state of the art was the classic exact algorithm of Even and Shiloach (1981), which is optimal under some assumptions (Roditty and Zwick 2011; Henzinger et al. 2015). Our result is the first to show that, in the incremental setting, this bound can be beaten in certain cases if some approximation is allowed." acknowledgement: "We thank the reviewers of ICALP 2013 for pointing to related articles and to an error in an example\r\ngiven in a previous version of this article. We also thank one of the reviewers of Transactions on\r\nAlgorithms for very detailed comments." article_number: '51' article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks. ACM Transactions on Algorithms. 2017;13(4). doi:10.1145/3146550 apa: Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2017). Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3146550 chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Maintenance of Breadth-First Spanning Trees in Partially Dynamic Networks.” ACM Transactions on Algorithms. Association for Computing Machinery, 2017. https://doi.org/10.1145/3146550. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks,” ACM Transactions on Algorithms, vol. 13, no. 4. Association for Computing Machinery, 2017. ista: Henzinger MH, Krinninger S, Nanongkai D. 2017. Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks. ACM Transactions on Algorithms. 13(4), 51. mla: Henzinger, Monika H., et al. “Sublinear-Time Maintenance of Breadth-First Spanning Trees in Partially Dynamic Networks.” ACM Transactions on Algorithms, vol. 13, no. 4, 51, Association for Computing Machinery, 2017, doi:10.1145/3146550. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, ACM Transactions on Algorithms 13 (2017). date_created: 2022-07-27T11:37:23Z date_published: 2017-10-01T00:00:00Z date_updated: 2022-09-09T11:57:42Z day: '01' doi: 10.1145/3146550 extern: '1' external_id: arxiv: - '1512.08147' intvolume: ' 13' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1512.08147 month: '10' oa: 1 oa_version: Preprint publication: ACM Transactions on Algorithms publication_identifier: eissn: - 1549-6333 issn: - 1549-6325 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Sublinear-time maintenance of breadth-first spanning trees in partially dynamic networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '11676' 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 algorithms. 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. acknowledgement: "The research leading to these results has received funding from the European Research\r\nCouncil under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement No. 340506." article_processing_charge: No article_type: original author: - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: David P. full_name: Williamson, David P. last_name: Williamson citation: ama: Dvořák W, Henzinger MH, Williamson DP. Maximizing a submodular function with viability constraints. Algorithmica. 2017;77(1):152-172. doi:10.1007/s00453-015-0066-y apa: Dvořák, W., Henzinger, M. H., & Williamson, D. P. (2017). Maximizing a submodular function with viability constraints. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-015-0066-y chicago: Dvořák, Wolfgang, Monika H Henzinger, and David P. Williamson. “Maximizing a Submodular Function with Viability Constraints.” Algorithmica. Springer Nature, 2017. https://doi.org/10.1007/s00453-015-0066-y. ieee: W. Dvořák, M. H. Henzinger, and D. P. Williamson, “Maximizing a submodular function with viability constraints,” Algorithmica, vol. 77, no. 1. Springer Nature, pp. 152–172, 2017. ista: Dvořák W, Henzinger MH, Williamson DP. 2017. Maximizing a submodular function with viability constraints. Algorithmica. 77(1), 152–172. mla: Dvořák, Wolfgang, et al. “Maximizing a Submodular Function with Viability Constraints.” Algorithmica, vol. 77, no. 1, Springer Nature, 2017, pp. 152–72, doi:10.1007/s00453-015-0066-y. short: W. Dvořák, M.H. Henzinger, D.P. Williamson, Algorithmica 77 (2017) 152–172. date_created: 2022-07-27T14:37:24Z date_published: 2017-01-01T00:00:00Z date_updated: 2022-09-12T08:58:16Z day: '01' doi: 10.1007/s00453-015-0066-y extern: '1' external_id: arxiv: - '1611.05753' intvolume: ' 77' issue: '1' keyword: - Approximation algorithms - Submodular functions - Phylogenetic diversity - Viability constraints language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.05753 month: '01' oa: 1 oa_version: Preprint page: 152-172 publication: Algorithmica publication_identifier: eissn: - 1432-0541 issn: - 0178-4617 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Maximizing a submodular function with viability constraints type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2017' ... --- _id: '1175' abstract: - lang: eng text: We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure. alternative_title: - LIPIcs author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Susanna full_name: De Rezende, Susanna last_name: De Rezende - first_name: Jakob full_name: Nordstrom, Jakob last_name: Nordstrom - first_name: Marc full_name: Vinyals, Marc last_name: Vinyals citation: ama: 'Alwen JF, De Rezende S, Nordstrom J, Vinyals M. Cumulative space in black-white pebbling and resolution. In: Papadimitriou C, ed. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:38:1-38-21. doi:10.4230/LIPIcs.ITCS.2017.38' apa: 'Alwen, J. F., De Rezende, S., Nordstrom, J., & Vinyals, M. (2017). Cumulative space in black-white pebbling and resolution. In C. Papadimitriou (Ed.) (Vol. 67, p. 38:1-38-21). Presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2017.38' chicago: Alwen, Joel F, Susanna De Rezende, Jakob Nordstrom, and Marc Vinyals. “Cumulative Space in Black-White Pebbling and Resolution.” edited by Christos Papadimitriou, 67:38:1-38-21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ITCS.2017.38. ieee: 'J. F. Alwen, S. De Rezende, J. Nordstrom, and M. Vinyals, “Cumulative space in black-white pebbling and resolution,” presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States, 2017, vol. 67, p. 38:1-38-21.' ista: 'Alwen JF, De Rezende S, Nordstrom J, Vinyals M. 2017. Cumulative space in black-white pebbling and resolution. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 67, 38:1-38-21.' mla: Alwen, Joel F., et al. Cumulative Space in Black-White Pebbling and Resolution. Edited by Christos Papadimitriou, vol. 67, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21, doi:10.4230/LIPIcs.ITCS.2017.38. short: J.F. Alwen, S. De Rezende, J. Nordstrom, M. Vinyals, in:, C. Papadimitriou (Ed.), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21. conference: end_date: 2017-01-11 location: Berkeley, CA, United States name: 'ITCS: Innovations in Theoretical Computer Science' start_date: 2017-01-09 date_created: 2018-12-11T11:50:33Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T06:48:51Z day: '01' ddc: - '005' - '600' department: - _id: KrPi doi: 10.4230/LIPIcs.ITCS.2017.38 editor: - first_name: Christos full_name: Papadimitriou, Christos last_name: Papadimitriou file: - access_level: open_access checksum: dbc94810be07c2fb1945d5c2a6130e6c content_type: application/pdf creator: system date_created: 2018-12-12T10:17:11Z date_updated: 2020-07-14T12:44:37Z file_id: '5263' file_name: IST-2018-927-v1+1_LIPIcs-ITCS-2017-38.pdf file_size: 557769 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 67' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 38:1-38-21 publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6179' pubrep_id: '927' quality_controlled: '1' scopus_import: 1 status: public title: Cumulative space in black-white pebbling and resolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2017' ... --- _id: '11772' abstract: - lang: eng text: A dynamic graph algorithm is a data structure that supports operations on dynamically changing graphs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Henzinger MH. The state of the art in dynamic graph algorithms. In: 44th International Conference on Current Trends in Theory and Practice of Computer Science. Vol 10706. Springer Nature; 2017:40–44. doi:10.1007/978-3-319-73117-9_3' apa: 'Henzinger, M. H. (2017). The state of the art in dynamic graph algorithms. In 44th International Conference on Current Trends in Theory and Practice of Computer Science (Vol. 10706, pp. 40–44). Krems, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-73117-9_3' chicago: Henzinger, Monika H. “The State of the Art in Dynamic Graph Algorithms.” In 44th International Conference on Current Trends in Theory and Practice of Computer Science, 10706:40–44. Springer Nature, 2017. https://doi.org/10.1007/978-3-319-73117-9_3. ieee: M. H. Henzinger, “The state of the art in dynamic graph algorithms,” in 44th International Conference on Current Trends in Theory and Practice of Computer Science, Krems, Austria, 2017, vol. 10706, pp. 40–44. ista: 'Henzinger MH. 2017. The state of the art in dynamic graph algorithms. 44th International Conference on Current Trends in Theory and Practice of Computer Science. SOFSEM: Theory and Practice of Computer Science, LNCS, vol. 10706, 40–44.' mla: Henzinger, Monika H. “The State of the Art in Dynamic Graph Algorithms.” 44th International Conference on Current Trends in Theory and Practice of Computer Science, vol. 10706, Springer Nature, 2017, pp. 40–44, doi:10.1007/978-3-319-73117-9_3. short: M.H. Henzinger, in:, 44th International Conference on Current Trends in Theory and Practice of Computer Science, Springer Nature, 2017, pp. 40–44. conference: end_date: 2018-02-02 location: Krems, Austria name: 'SOFSEM: Theory and Practice of Computer Science' start_date: 2018-01-29 date_created: 2022-08-08T13:16:37Z date_published: 2017-12-22T00:00:00Z date_updated: 2023-02-10T08:36:03Z day: '22' doi: 10.1007/978-3-319-73117-9_3 extern: '1' intvolume: ' 10706' language: - iso: eng month: '12' oa_version: None page: 40–44 publication: 44th International Conference on Current Trends in Theory and Practice of Computer Science publication_identifier: eisbn: - '9783319731179' isbn: - '9783319731162' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The state of the art in dynamic graph algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10706 year: '2017' ... --- _id: '11829' abstract: - lang: eng text: "In recent years it has become popular to study dynamic problems in a sensitivity setting: Instead of allowing for an arbitrary sequence of updates, the sensitivity model only allows to apply batch updates of small size to the original input data. The sensitivity model is particularly appealing since recent strong conditional lower bounds ruled out fast algorithms for many dynamic problems, such as shortest paths, reachability, or subgraph connectivity.\r\n\r\nIn this paper we prove conditional lower bounds for these and additional problems in a sensitivity setting. For example, we show that under the Boolean Matrix Multiplication (BMM) conjecture combinatorial algorithms cannot compute the (4/3-\\varepsilon)-approximate diameter of an undirected unweighted dense graph with truly subcubic preprocessing time and truly subquadratic update/query time. This result is surprising since in the static setting it is not clear whether a reduction from BMM to diameter is possible. We further show under the BMM conjecture that many problems, such as reachability or approximate shortest paths, cannot be solved faster than by recomputation from scratch even after only one or two edge insertions. We extend our reduction from BMM to Diameter to give a reduction from All Pairs Shortest Paths to Diameter under one deletion in weighted graphs. This is intriguing, as in the static setting it is a big open problem whether Diameter is as hard as APSP. We further get a nearly tight lower bound for shortest paths after two edge deletions based on the APSP conjecture. We give more lower bounds under the Strong Exponential Time Hypothesis. Many of our lower bounds also hold for static oracle data structures where no sensitivity is required.\r\n\r\nFinally, we give the first algorithm for the (1+\\varepsilon)-approximate radius, diameter, and eccentricity problems in directed or undirected unweighted graphs in case of single edges failures. The algorithm has a truly subcubic running time for graphs with a truly subquadratic number of edges; it is tight w.r.t. the conditional lower bounds we obtain." alternative_title: - LIPIcs article_number: '26' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Andrea full_name: Lincoln, Andrea last_name: Lincoln - first_name: Stefan full_name: Neumann, Stefan last_name: Neumann - first_name: Virginia full_name: Vassilevska Williams, Virginia last_name: Vassilevska Williams citation: ama: 'Henzinger MH, Lincoln A, Neumann S, Vassilevska Williams V. Conditional hardness for sensitivity problems. In: 8th Innovations in Theoretical Computer Science Conference. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ITCS.2017.26' apa: 'Henzinger, M. H., Lincoln, A., Neumann, S., & Vassilevska Williams, V. (2017). Conditional hardness for sensitivity problems. In 8th Innovations in Theoretical Computer Science Conference (Vol. 67). Berkley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2017.26' chicago: Henzinger, Monika H, Andrea Lincoln, Stefan Neumann, and Virginia Vassilevska Williams. “Conditional Hardness for Sensitivity Problems.” In 8th Innovations in Theoretical Computer Science Conference, Vol. 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ITCS.2017.26. ieee: M. H. Henzinger, A. Lincoln, S. Neumann, and V. Vassilevska Williams, “Conditional hardness for sensitivity problems,” in 8th Innovations in Theoretical Computer Science Conference, Berkley, CA, United States, 2017, vol. 67. ista: 'Henzinger MH, Lincoln A, Neumann S, Vassilevska Williams V. 2017. Conditional hardness for sensitivity problems. 8th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science Conference, LIPIcs, vol. 67, 26.' mla: Henzinger, Monika H., et al. “Conditional Hardness for Sensitivity Problems.” 8th Innovations in Theoretical Computer Science Conference, vol. 67, 26, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ITCS.2017.26. short: M.H. Henzinger, A. Lincoln, S. Neumann, V. Vassilevska Williams, in:, 8th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-01-11 location: Berkley, CA, United States name: 'ITCS: Innovations in Theoretical Computer Science Conference' start_date: 2017-01-09 date_created: 2022-08-12T08:55:33Z date_published: 2017-11-28T00:00:00Z date_updated: 2023-02-16T11:49:15Z day: '28' doi: 10.4230/LIPICS.ITCS.2017.26 extern: '1' external_id: arxiv: - '1703.01638' intvolume: ' 67' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.ITCS.2017.26 month: '11' oa: 1 oa_version: Published Version publication: 8th Innovations in Theoretical Computer Science Conference publication_identifier: isbn: - '9783959770293' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Conditional hardness for sensitivity problems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2017' ... --- _id: '11833' abstract: - lang: eng text: "We introduce a new algorithmic framework for designing dynamic graph algorithms in minor-free graphs, by exploiting the structure of such graphs and a tool called vertex sparsification, which is a way to compress large graphs into small ones that well preserve relevant properties among a subset of vertices and has previously mainly been used in the design of approximation algorithms.\r\n\r\nUsing this framework, we obtain a Monte Carlo randomized fully dynamic algorithm for (1 + epsilon)-approximating the energy of electrical flows in n-vertex planar graphs with tilde{O}(r epsilon^{-2}) worst-case update time and tilde{O}((r + n / sqrt{r}) epsilon^{-2}) worst-case query time, for any r larger than some constant. For r=n^{2/3}, this gives tilde{O}(n^{2/3} epsilon^{-2}) update time and tilde{O}(n^{2/3} epsilon^{-2}) query time. We also extend this algorithm to work for minor-free graphs with similar approximation and running time guarantees. Furthermore, we illustrate our framework on the all-pairs max flow and shortest path problems by giving corresponding dynamic algorithms in minor-free graphs with both sublinear update and query times. To the best of our knowledge, our results are the first to systematically establish such a connection between dynamic graph algorithms and vertex sparsification.\r\n\r\nWe also present both upper bound and lower bound for maintaining the energy of electrical flows in the incremental subgraph model, where updates consist of only vertex activations, which might be of independent interest." alternative_title: - LIPIcs article_number: '45' article_processing_charge: No author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Pan full_name: Peng, Pan last_name: Peng citation: ama: 'Goranci G, Henzinger MH, Peng P. The power of vertex sparsifiers in dynamic graph algorithms. In: 25th Annual European Symposium on Algorithms. Vol 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ESA.2017.45' apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2017). The power of vertex sparsifiers in dynamic graph algorithms. In 25th Annual European Symposium on Algorithms (Vol. 87). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2017.45' chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “The Power of Vertex Sparsifiers in Dynamic Graph Algorithms.” In 25th Annual European Symposium on Algorithms, Vol. 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ESA.2017.45. ieee: G. Goranci, M. H. Henzinger, and P. Peng, “The power of vertex sparsifiers in dynamic graph algorithms,” in 25th Annual European Symposium on Algorithms, Vienna, Austria, 2017, vol. 87. ista: 'Goranci G, Henzinger MH, Peng P. 2017. The power of vertex sparsifiers in dynamic graph algorithms. 25th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 87, 45.' mla: Goranci, Gramoz, et al. “The Power of Vertex Sparsifiers in Dynamic Graph Algorithms.” 25th Annual European Symposium on Algorithms, vol. 87, 45, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ESA.2017.45. short: G. Goranci, M.H. Henzinger, P. Peng, in:, 25th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-06 location: Vienna, Austria name: 'ESA: Annual European Symposium on Algorithms' start_date: 2017-09-04 date_created: 2022-08-12T10:46:26Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-16T11:56:37Z day: '01' doi: 10.4230/LIPICS.ESA.2017.45 extern: '1' external_id: arxiv: - '1712.06473' intvolume: ' 87' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2017.45 month: '09' oa: 1 oa_version: Published Version publication: 25th Annual European Symposium on Algorithms publication_identifier: isbn: - 978-3-95977-049-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: The power of vertex sparsifiers in dynamic graph algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2017' ... --- _id: '11832' abstract: - lang: eng text: "In this paper, we study the problem of opening centers to cluster a set of clients in a metric space so as to minimize the sum of the costs of the centers and of the cluster radii, in a dynamic environment where clients arrive and depart, and the solution must be updated efficiently while remaining competitive with respect to the current optimal solution. We call this dynamic sum-of-radii clustering problem.\r\n\r\nWe present a data structure that maintains a solution whose cost is within a constant factor of the cost of an optimal solution in metric spaces with bounded doubling dimension and whose worst-case update time is logarithmic in the parameters of the problem." alternative_title: - LIPIcs article_number: '48' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Dariusz full_name: Leniowski, Dariusz last_name: Leniowski - first_name: Claire full_name: Mathieu, Claire last_name: Mathieu citation: ama: 'Henzinger MH, Leniowski D, Mathieu C. Dynamic clustering to minimize the sum of radii. In: 25th Annual European Symposium on Algorithms. Vol 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ESA.2017.48' apa: 'Henzinger, M. H., Leniowski, D., & Mathieu, C. (2017). Dynamic clustering to minimize the sum of radii. In 25th Annual European Symposium on Algorithms (Vol. 87). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2017.48' chicago: Henzinger, Monika H, Dariusz Leniowski, and Claire Mathieu. “Dynamic Clustering to Minimize the Sum of Radii.” In 25th Annual European Symposium on Algorithms, Vol. 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ESA.2017.48. ieee: M. H. Henzinger, D. Leniowski, and C. Mathieu, “Dynamic clustering to minimize the sum of radii,” in 25th Annual European Symposium on Algorithms, Vienna, Austria, 2017, vol. 87. ista: 'Henzinger MH, Leniowski D, Mathieu C. 2017. Dynamic clustering to minimize the sum of radii. 25th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 87, 48.' mla: Henzinger, Monika H., et al. “Dynamic Clustering to Minimize the Sum of Radii.” 25th Annual European Symposium on Algorithms, vol. 87, 48, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ESA.2017.48. short: M.H. Henzinger, D. Leniowski, C. Mathieu, in:, 25th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-06 location: Vienna, Austria name: 'ESA: Annual European Symposium on Algorithms' start_date: 2017-09-04 date_created: 2022-08-12T09:58:46Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-16T11:54:12Z day: '01' doi: 10.4230/LIPICS.ESA.2017.48 extern: '1' external_id: arxiv: - '1707.02577' intvolume: ' 87' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.ESA.2017.48 month: '09' oa: 1 oa_version: Published Version publication: 25th Annual European Symposium on Algorithms publication_identifier: isbn: - 978-3-95977-049-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Dynamic clustering to minimize the sum of radii type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2017' ... --- _id: '11874' abstract: - lang: eng text: "We consider the problem of maintaining an approximately maximum (fractional) matching and an approximately minimum vertex cover in a dynamic graph. Starting with the seminal paper by Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. There remains, however, a polynomial gap between the best known worst case update time and the best known amortised update time for this problem, even after allowing for randomisation. Specifically, Bernstein and Stein [ICALP 2015, SODA 2016] have the best known worst case update time. They present a deterministic data structure with approximation ratio (3/2 + ∊) and worst case update time O(m1/4/ ∊2), where m is the number of edges in the graph. In recent past, Gupta and Peng [FOCS 2013] gave a deterministic data structure with approximation ratio (1+ ∊) and worst case update time No known randomised data structure beats the worst case update times of these two results. In contrast, the paper by Onak and Rubinfeld [STOC 2010] gave a randomised data structure with approximation ratio O(1) and amortised update time O(log2 n), where n is the number of nodes in the graph. This was later improved by Baswana, Gupta and Sen [FOCS 2011] and Solomon [FOCS 2016], leading to a randomised date structure with approximation ratio 2 and amortised update time O(1).\r\n\r\nWe bridge the polynomial gap between the worst case and amortised update times for this problem, without using any randomisation. We present a deterministic data structure with approximation ratio (2 + ∊) and worst case update time O(log3 n), for all sufficiently small constants ∊." article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Bhattacharya S, Henzinger MH, Nanongkai D. Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time. In: 28th Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 0. Society for Industrial and Applied Mathematics; 2017:470-489. doi:10.1137/1.9781611974782.30' apa: 'Bhattacharya, S., Henzinger, M. H., & Nanongkai, D. (2017). Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time. In 28th Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 0, pp. 470–489). Barcelona, Spain: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611974782.30' chicago: Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “Fully Dynamic Approximate Maximum Matching and Minimum Vertex Cover in o(Log3 n) Worst Case Update Time.” In 28th Annual ACM-SIAM Symposium on Discrete Algorithms, 0:470–89. Society for Industrial and Applied Mathematics, 2017. https://doi.org/10.1137/1.9781611974782.30. ieee: S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time,” in 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Barcelona, Spain, 2017, vol. 0, pp. 470–489. ista: 'Bhattacharya S, Henzinger MH, Nanongkai D. 2017. Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time. 28th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 0, 470–489.' mla: Bhattacharya, Sayan, et al. “Fully Dynamic Approximate Maximum Matching and Minimum Vertex Cover in o(Log3 n) Worst Case Update Time.” 28th Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 0, Society for Industrial and Applied Mathematics, 2017, pp. 470–89, doi:10.1137/1.9781611974782.30. short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2017, pp. 470–489. conference: end_date: 2017-01-19 location: Barcelona, Spain name: 'SODA: Symposium on Discrete Algorithms' start_date: 2017-01-16 date_created: 2022-08-16T12:28:27Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-17T11:54:22Z day: '01' doi: 10.1137/1.9781611974782.30 extern: '1' external_id: arxiv: - '1704.02844' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.02844 month: '01' oa: 1 oa_version: Preprint page: 470 - 489 publication: 28th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-161197478-2 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Fully dynamic approximate maximum matching and minimum vertex cover in o(log3 n) worst case update time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: '0' year: '2017' ... --- _id: '11873' abstract: - lang: eng text: "We study the problem of computing a minimum cut in a simple, undirected graph and give a deterministic O(m log2 n log log2 n) time algorithm. This improves both on the best previously known deterministic running time of O(m log12 n) (Kawarabayashi and Thorup [12]) and the best previously known randomized running time of O(mlog3n) (Karger [11]) for this problem, though Karger's algorithm can be further applied to weighted graphs.\r\n\r\nOur approach is using the Kawarabayashi and Tho- rup graph compression technique, which repeatedly finds low-conductance cuts. To find these cuts they use a diffusion-based local algorithm. We use instead a flow- based local algorithm and suitably adjust their framework to work with our flow-based subroutine. Both flow and diffusion based methods have a long history of being applied to finding low conductance cuts. Diffusion algorithms have several variants that are naturally local while it is more complicated to make flow methods local. Some prior work has proven nice properties for local flow based algorithms with respect to improving or cleaning up low conductance cuts. Our flow subroutine, however, is the first that is both local and produces low conductance cuts. Thus, it may be of independent interest." article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Satish full_name: Rao, Satish last_name: Rao - first_name: Di full_name: Wang, Di last_name: Wang citation: ama: 'Henzinger MH, Rao S, Wang D. Local flow partitioning for faster edge connectivity. In: 28th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2017:1919-1938. doi:10.1137/1.9781611974782.125' apa: 'Henzinger, M. H., Rao, S., & Wang, D. (2017). Local flow partitioning for faster edge connectivity. In 28th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1919–1938). Barcelona, Spain: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611974782.125' chicago: Henzinger, Monika H, Satish Rao, and Di Wang. “Local Flow Partitioning for Faster Edge Connectivity.” In 28th Annual ACM-SIAM Symposium on Discrete Algorithms, 1919–38. Society for Industrial and Applied Mathematics, 2017. https://doi.org/10.1137/1.9781611974782.125. ieee: M. H. Henzinger, S. Rao, and D. Wang, “Local flow partitioning for faster edge connectivity,” in 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Barcelona, Spain, 2017, pp. 1919–1938. ista: 'Henzinger MH, Rao S, Wang D. 2017. Local flow partitioning for faster edge connectivity. 28th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1919–1938.' mla: Henzinger, Monika H., et al. “Local Flow Partitioning for Faster Edge Connectivity.” 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2017, pp. 1919–38, doi:10.1137/1.9781611974782.125. short: M.H. Henzinger, S. Rao, D. Wang, in:, 28th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2017, pp. 1919–1938. conference: end_date: 2017-01-19 location: Barcelona, Spain name: 'SODA: Symposium on Discrete Algorithms' start_date: 2017-01-16 date_created: 2022-08-16T12:20:59Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-21T16:32:01Z day: '01' doi: 10.1137/1.9781611974782.125 extern: '1' external_id: arxiv: - '1704.01254' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.01254 month: '01' oa: 1 oa_version: Preprint page: 1919-1938 publication: 28th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-161197478-2 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '11889' relation: earlier_version status: public scopus_import: '1' status: public title: Local flow partitioning for faster edge connectivity type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '11831' abstract: - lang: eng text: "Graph Sparsification aims at compressing large graphs into smaller ones while (approximately) preserving important characteristics of the input graph. In this work we study Vertex Sparsifiers, i.e., sparsifiers whose goal is to reduce the number of vertices. Given a weighted graph G=(V,E), and a terminal set K with |K|=k, a quality-q vertex cut sparsifier of G is a graph H with K contained in V_H that preserves the value of minimum cuts separating any bipartition of K, up to a factor of q. We show that planar graphs with all the k terminals lying on the same face admit quality-1 vertex cut sparsifier of size O(k^2) that are also planar. Our result extends to vertex flow and distance sparsifiers. It improves the previous best known bound of O(k^2 2^(2k)) for cut and flow sparsifiers by an exponential factor, and matches an Omega(k^2) lower-bound for this class of graphs.\r\n\r\nWe also study vertex reachability sparsifiers for directed graphs. Given a digraph G=(V,E) and a terminal set K, a vertex reachability sparsifier of G is a digraph H=(V_H,E_H), K contained in V_H that preserves all reachability information among terminal pairs. We introduce the notion of reachability-preserving minors, i.e., we require H to be a minor of G. Among others, for general planar digraphs, we construct reachability-preserving minors of size O(k^2 log^2 k). We complement our upper-bound by showing that there exists an infinite family of acyclic planar digraphs such that any reachability-preserving minor must have Omega(k^2) vertices." alternative_title: - LIPIcs article_number: '44' article_processing_charge: No author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Pan full_name: Peng, Pan last_name: Peng citation: ama: 'Goranci G, Henzinger MH, Peng P. Improved guarantees for vertex sparsification in planar graphs. In: 25th Annual European Symposium on Algorithms. Vol 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ESA.2017.44' apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2017). Improved guarantees for vertex sparsification in planar graphs. In 25th Annual European Symposium on Algorithms (Vol. 87). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2017.44' chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Improved Guarantees for Vertex Sparsification in Planar Graphs.” In 25th Annual European Symposium on Algorithms, Vol. 87. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ESA.2017.44. ieee: G. Goranci, M. H. Henzinger, and P. Peng, “Improved guarantees for vertex sparsification in planar graphs,” in 25th Annual European Symposium on Algorithms, Vienna, Austria, 2017, vol. 87. ista: 'Goranci G, Henzinger MH, Peng P. 2017. Improved guarantees for vertex sparsification in planar graphs. 25th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 87, 44.' mla: Goranci, Gramoz, et al. “Improved Guarantees for Vertex Sparsification in Planar Graphs.” 25th Annual European Symposium on Algorithms, vol. 87, 44, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ESA.2017.44. short: G. Goranci, M.H. Henzinger, P. Peng, in:, 25th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-06 location: Vienna, Austria name: 'ESA: Annual European Symposium on Algorithms' start_date: 2017-09-04 date_created: 2022-08-12T09:27:11Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-21T16:32:16Z day: '01' doi: 10.4230/LIPICS.ESA.2017.44 extern: '1' external_id: arxiv: - '1702.01136' intvolume: ' 87' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2017.44 month: '09' oa: 1 oa_version: Published Version publication: 25th Annual European Symposium on Algorithms publication_identifier: isbn: - 978-3-95977-049-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '11894' relation: later_version status: public scopus_import: '1' status: public title: Improved guarantees for vertex sparsification in planar graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2017' ... --- _id: '11903' abstract: - lang: eng text: "Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1−1/e). (2) On the positive side we present (i) an \U0001D442(\U0001D45B√)-approximation algorithm for general concave externality functions, (ii) an O(log m)-approximation algorithm for linear externality functions, and (iii) a 518(1−1/\U0001D452)-approximation algorithm for 2-hop step function externalities. We also improve the result from [7] for 1-hop step function externalities by giving a 12(1−1/\U0001D452)-approximation algorithm." article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: Bhattacharya S, Dvořák W, Henzinger MH, Starnberger M. Welfare maximization with friends-of-friends network externalities. Theory of Computing Systems. 2017;61(4):948-986. doi:10.1007/s00224-017-9759-8 apa: Bhattacharya, S., Dvořák, W., Henzinger, M. H., & Starnberger, M. (2017). Welfare maximization with friends-of-friends network externalities. Theory of Computing Systems. Springer Nature. https://doi.org/10.1007/s00224-017-9759-8 chicago: Bhattacharya, Sayan, Wolfgang Dvořák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” Theory of Computing Systems. Springer Nature, 2017. https://doi.org/10.1007/s00224-017-9759-8. ieee: S. Bhattacharya, W. Dvořák, M. H. Henzinger, and M. Starnberger, “Welfare maximization with friends-of-friends network externalities,” Theory of Computing Systems, vol. 61, no. 4. Springer Nature, pp. 948–986, 2017. ista: Bhattacharya S, Dvořák W, Henzinger MH, Starnberger M. 2017. Welfare maximization with friends-of-friends network externalities. Theory of Computing Systems. 61(4), 948–986. mla: Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” Theory of Computing Systems, vol. 61, no. 4, Springer Nature, 2017, pp. 948–86, doi:10.1007/s00224-017-9759-8. short: S. Bhattacharya, W. Dvořák, M.H. Henzinger, M. Starnberger, Theory of Computing Systems 61 (2017) 948–986. date_created: 2022-08-17T11:14:12Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-02-21T16:29:58Z day: '01' doi: 10.1007/s00224-017-9759-8 extern: '1' intvolume: ' 61' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00224-017-9759-8 month: '11' oa: 1 oa_version: Published Version page: 948-986 publication: Theory of Computing Systems publication_identifier: eissn: - 1433-0490 issn: - 1432-4350 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11837' relation: earlier_version status: public scopus_import: '1' status: public title: Welfare maximization with friends-of-friends network externalities type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2017' ... --- _id: '1191' abstract: - lang: eng text: Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed. acknowledgement: "We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project." author: - first_name: Richard full_name: Kollár, Richard last_name: Kollár - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak citation: ama: Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3 apa: Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3 chicago: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3. ieee: R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017. ista: Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559. mla: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3. short: R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559. date_created: 2018-12-11T11:50:38Z date_published: 2017-03-01T00:00:00Z date_updated: 2021-01-12T06:48:58Z day: '01' department: - _id: NiBa doi: 10.1007/s11538-016-0244-3 ec_funded: 1 intvolume: ' 79' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.00944 month: '03' oa: 1 oa_version: Preprint page: 525-559 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Bulletin of Mathematical Biology publication_status: published publisher: Springer publist_id: '6160' quality_controlled: '1' scopus_import: 1 status: public title: Existence of traveling waves for the generalized F–KPP equation type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2017' ... --- _id: '11961' abstract: - lang: eng text: Flow chemistry involves the use of channels or tubing to conduct a reaction in a continuous stream rather than in a flask. Flow equipment provides chemists with unique control over reaction parameters enhancing reactivity or in some cases enabling new reactions. This relatively young technology has received a remarkable amount of attention in the past decade with many reports on what can be done in flow. Until recently, however, the question, “Should we do this in flow?” has merely been an afterthought. This review introduces readers to the basic principles and fundamentals of flow chemistry and critically discusses recent flow chemistry accounts. article_processing_charge: No article_type: original author: - first_name: Matthew B. full_name: Plutschack, Matthew B. last_name: Plutschack - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Kerry full_name: Gilmore, Kerry last_name: Gilmore - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger citation: ama: Plutschack MB, Pieber B, Gilmore K, Seeberger PH. The Hitchhiker’s Guide to flow chemistry. Chemical Reviews. 2017;117(18):11796-11893. doi:10.1021/acs.chemrev.7b00183 apa: Plutschack, M. B., Pieber, B., Gilmore, K., & Seeberger, P. H. (2017). The Hitchhiker’s Guide to flow chemistry. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00183 chicago: Plutschack, Matthew B., Bartholomäus Pieber, Kerry Gilmore, and Peter H. Seeberger. “The Hitchhiker’s Guide to Flow Chemistry.” Chemical Reviews. American Chemical Society, 2017. https://doi.org/10.1021/acs.chemrev.7b00183. ieee: M. B. Plutschack, B. Pieber, K. Gilmore, and P. H. Seeberger, “The Hitchhiker’s Guide to flow chemistry,” Chemical Reviews, vol. 117, no. 18. American Chemical Society, pp. 11796–11893, 2017. ista: Plutschack MB, Pieber B, Gilmore K, Seeberger PH. 2017. The Hitchhiker’s Guide to flow chemistry. Chemical Reviews. 117(18), 11796–11893. mla: Plutschack, Matthew B., et al. “The Hitchhiker’s Guide to Flow Chemistry.” Chemical Reviews, vol. 117, no. 18, American Chemical Society, 2017, pp. 11796–893, doi:10.1021/acs.chemrev.7b00183. short: M.B. Plutschack, B. Pieber, K. Gilmore, P.H. Seeberger, Chemical Reviews 117 (2017) 11796–11893. date_created: 2022-08-24T11:07:46Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-21T10:09:28Z day: '01' doi: 10.1021/acs.chemrev.7b00183 extern: '1' external_id: pmid: - '28570059' intvolume: ' 117' issue: '18' language: - iso: eng month: '06' oa_version: None page: 11796-11893 pmid: 1 publication: Chemical Reviews publication_identifier: eissn: - 1520-6890 issn: - 0009-2665 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: The Hitchhiker’s Guide to flow chemistry type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2017' ... --- _id: '11976' abstract: - lang: eng text: The way organic multistep synthesis is performed is changing due to the adoption of flow chemical techniques, which has enabled the development of improved methods to make complex molecules. The modular nature of the technique provides not only access to target molecules via linear flow approaches but also for the targeting of structural cores with single systems. This perspective article summarizes the state of the art of continuous multistep synthesis and discusses the main challenges and opportunities in this area. article_processing_charge: No article_type: original author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Kerry full_name: Gilmore, Kerry last_name: Gilmore - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger citation: ama: Pieber B, Gilmore K, Seeberger PH. Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. 2017;7(3-4):129-136. doi:10.1556/1846.2017.00016 apa: Pieber, B., Gilmore, K., & Seeberger, P. H. (2017). Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. AKJournals. https://doi.org/10.1556/1846.2017.00016 chicago: Pieber, Bartholomäus, Kerry Gilmore, and Peter H. Seeberger. “Integrated Flow Processing - Challenges in Continuous Multistep Synthesis.” Journal of Flow Chemistry. AKJournals, 2017. https://doi.org/10.1556/1846.2017.00016. ieee: B. Pieber, K. Gilmore, and P. H. Seeberger, “Integrated flow processing - challenges in continuous multistep synthesis,” Journal of Flow Chemistry, vol. 7, no. 3–4. AKJournals, pp. 129–136, 2017. ista: Pieber B, Gilmore K, Seeberger PH. 2017. Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. 7(3–4), 129–136. mla: Pieber, Bartholomäus, et al. “Integrated Flow Processing - Challenges in Continuous Multistep Synthesis.” Journal of Flow Chemistry, vol. 7, no. 3–4, AKJournals, 2017, pp. 129–36, doi:10.1556/1846.2017.00016. short: B. Pieber, K. Gilmore, P.H. Seeberger, Journal of Flow Chemistry 7 (2017) 129–136. date_created: 2022-08-25T10:47:51Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-02-21T10:10:02Z day: '01' doi: 10.1556/1846.2017.00016 extern: '1' intvolume: ' 7' issue: 3-4 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1556/1846.2017.00016 month: '09' oa: 1 oa_version: Published Version page: 129-136 publication: Journal of Flow Chemistry publication_identifier: eissn: - 2063-0212 issn: - 2062-249X publication_status: published publisher: AKJournals quality_controlled: '1' scopus_import: '1' status: public title: Integrated flow processing - challenges in continuous multistep synthesis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2017' ... --- _id: '1211' abstract: - lang: eng text: Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here. acknowledgement: 'This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ' author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Predrag full_name: Cvitanović, Predrag last_name: Cvitanović citation: ama: Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z apa: Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z chicago: Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z. ieee: N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655, 2017. ista: Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655. mla: Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:10.1007/s10955-016-1672-z. short: N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655. date_created: 2018-12-11T11:50:44Z date_published: 2017-05-01T00:00:00Z date_updated: 2021-01-12T06:49:07Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.1007/s10955-016-1672-z file: - access_level: open_access checksum: 3e971d09eb167761aa0888ed415b0056 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:01Z date_updated: 2020-07-14T12:44:39Z file_id: '5319' file_name: IST-2017-782-v1+1_BudCvi15.pdf file_size: 2820207 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 167' issue: 3-4 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 636-655 publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '6136' pubrep_id: '782' quality_controlled: '1' scopus_import: 1 status: public title: Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 167 year: '2017' ... --- _id: '123' abstract: - lang: eng text: The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics. acknowledgement: A.S. acknowledges funding from the Delta Institute for Theoretical Physics and the hospitality of the IBS Center for Theoretical Physics of Complex Systems, Daejeon, South Korea. We acknowledge funding from the Netherlands Organisation for Scientific Research through grants VICI No. NWO-680-47-609 (M.v.H. and S.R.W.), VENI No. NWO-680-47-445 (C.C.) and VENI No. NWO-680-47-453 (S.R.W.). author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Antal full_name: Zuiderwijk, Antal last_name: Zuiderwijk - first_name: Anton full_name: Souslov, Anton last_name: Souslov - first_name: Corentin full_name: Coulais, Corentin last_name: Coulais - first_name: Martin full_name: Van Hecke, Martin last_name: Van Hecke citation: ama: Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 2017;13(11):1095-1099. doi:10.1038/nphys4194 apa: Waitukaitis, S. R., Zuiderwijk, A., Souslov, A., Coulais, C., & Van Hecke, M. (2017). Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys4194 chicago: Waitukaitis, Scott R, Antal Zuiderwijk, Anton Souslov, Corentin Coulais, and Martin Van Hecke. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” Nature Physics. Nature Publishing Group, 2017. https://doi.org/10.1038/nphys4194. ieee: S. R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, and M. Van Hecke, “Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing,” Nature Physics, vol. 13, no. 11. Nature Publishing Group, pp. 1095–1099, 2017. ista: Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. 2017. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 13(11), 1095–1099. mla: Waitukaitis, Scott R., et al. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” Nature Physics, vol. 13, no. 11, Nature Publishing Group, 2017, pp. 1095–99, doi:10.1038/nphys4194. short: S.R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, M. Van Hecke, Nature Physics 13 (2017) 1095–1099. date_created: 2018-12-11T11:44:45Z date_published: 2017-07-24T00:00:00Z date_updated: 2021-01-12T06:49:14Z day: '24' doi: 10.1038/nphys4194 extern: '1' external_id: arxiv: - '1705.03530' intvolume: ' 13' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.03530 month: '07' oa: 1 oa_version: Preprint page: 1095 - 1099 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7931' quality_controlled: '1' status: public title: Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '12571' abstract: - lang: eng text: We consider the problems of maintaining approximate maximum matching and minimum vertex cover in a dynamic graph. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized 2-approximation dynamic algorithm for this problem that has amortized update time of O(1) with high probability. We consider the natural open question of derandomizing this result. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya, Henzinger and Italiano [SODA 2015]; it had an approximation ratio of (2+ϵ) and an amortized update time of O(logn/ϵ2). Our result can be generalized to give a fully dynamic O(f3)-approximation algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional matching problems, where every hyperedge has at most f vertices. alternative_title: - LNCS article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Deeparnab full_name: Chakrabarty, Deeparnab last_name: Chakrabarty - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Bhattacharya S, Chakrabarty D, Henzinger MH. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In: 19th International Conference on Integer Programming and Combinatorial Optimization. Vol 10328. Springer Nature; 2017:86-98. doi:10.1007/978-3-319-59250-3_8' apa: 'Bhattacharya, S., Chakrabarty, D., & Henzinger, M. H. (2017). Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In 19th International Conference on Integer Programming and Combinatorial Optimization (Vol. 10328, pp. 86–98). Waterloo, ON, Canada: Springer Nature. https://doi.org/10.1007/978-3-319-59250-3_8' chicago: Bhattacharya, Sayan, Deeparnab Chakrabarty, and Monika H Henzinger. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” In 19th International Conference on Integer Programming and Combinatorial Optimization, 10328:86–98. Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59250-3_8. ieee: S. Bhattacharya, D. Chakrabarty, and M. H. Henzinger, “Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time,” in 19th International Conference on Integer Programming and Combinatorial Optimization, Waterloo, ON, Canada, 2017, vol. 10328, pp. 86–98. ista: 'Bhattacharya S, Chakrabarty D, Henzinger MH. 2017. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. 19th International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 10328, 86–98.' mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” 19th International Conference on Integer Programming and Combinatorial Optimization, vol. 10328, Springer Nature, 2017, pp. 86–98, doi:10.1007/978-3-319-59250-3_8. short: S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, in:, 19th International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2017, pp. 86–98. conference: end_date: 2017-06-28 location: Waterloo, ON, Canada name: 'IPCO: Integer Programming and Combinatorial Optimization' start_date: 2017-06-26 date_created: 2023-02-20T07:52:31Z date_published: 2017-05-24T00:00:00Z date_updated: 2023-02-20T07:57:24Z day: '24' doi: 10.1007/978-3-319-59250-3_8 extern: '1' external_id: arxiv: - '1611.00198' intvolume: ' 10328' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.00198 month: '05' oa: 1 oa_version: Preprint page: 86-98 publication: 19th International Conference on Integer Programming and Combinatorial Optimization publication_identifier: eisbn: - '9783319592503' isbn: - '9783319592497' issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10328 year: '2017' ... --- _id: '1113' abstract: - lang: eng text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth.' article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Michael full_name: Pelsmajer, Michael last_name: Pelsmajer - first_name: Marcus full_name: Schaefer, Marcus last_name: Schaefer citation: ama: Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408 apa: Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408 chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408. ieee: R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017. ista: Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154. mla: Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408. short: R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154. date_created: 2018-12-11T11:50:13Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-02-23T10:05:57Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.7155/jgaa.00408 ec_funded: 1 external_id: arxiv: - '1608.08662' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-10-24T10:54:37Z date_updated: 2019-10-24T10:54:37Z file_id: '6967' file_name: 2017_JournalGraphAlgorithms_Fulek.pdf file_size: 573623 relation: main_file success: 1 file_date_updated: 2019-10-24T10:54:37Z has_accepted_license: '1' intvolume: ' 21' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 135 - 154 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Graph Algorithms and Applications publication_status: published publisher: Brown University publist_id: '6254' quality_controlled: '1' related_material: record: - id: '1164' relation: earlier_version status: public - id: '1595' relation: earlier_version status: public scopus_import: 1 status: public title: Hanani-Tutte for radial planarity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2017' ... --- _id: '169' abstract: - lang: eng text: We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Vinay full_name: Kumaraswamy, Vinay last_name: Kumaraswamy - first_name: Rapael full_name: Steiner, Rapael last_name: Steiner citation: ama: Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx116 apa: Browning, T. D., Kumaraswamy, V., & Steiner, R. (2017). Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx116 chicago: Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik Implies Optimal Covering Exponent for S3.” International Mathematics Research Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx116. ieee: T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal covering exponent for S3,” International Mathematics Research Notices. Oxford University Press, 2017. ista: Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. mla: Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent for S3.” International Mathematics Research Notices, Oxford University Press, 2017, doi:10.1093/imrn/rnx116. short: T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research Notices (2017). date_created: 2018-12-11T11:44:59Z date_published: 2017-06-19T00:00:00Z date_updated: 2021-01-12T06:52:32Z day: '19' doi: 10.1093/imrn/rnx116 extern: '1' external_id: arxiv: - '1609.06097' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.06097 month: '06' oa: 1 oa_version: None publication: International Mathematics Research Notices publication_status: published publisher: Oxford University Press publist_id: '7752' quality_controlled: '1' status: public title: Twisted Linnik implies optimal covering exponent for S3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '172' abstract: - lang: eng text: We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Damaris full_name: Schindler, Damaris last_name: Schindler citation: ama: Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx252 apa: Browning, T. D., & Schindler, D. (2017). Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx252 chicago: Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx252. ieee: T. D. Browning and D. Schindler, “Strong approximation and a conjecture of Harpaz and Wittenberg,” International Mathematics Research Notices. Oxford University Press, 2017. ista: Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. mla: Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices, Oxford University Press, 2017, doi:10.1093/imrn/rnx252. short: T.D. Browning, D. Schindler, International Mathematics Research Notices (2017). date_created: 2018-12-11T11:45:00Z date_published: 2017-10-30T00:00:00Z date_updated: 2021-01-12T06:52:45Z day: '30' doi: 10.1093/imrn/rnx252 extern: '1' external_id: arxiv: - '1509.07744' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.07744 month: '10' oa: 1 oa_version: None publication: International Mathematics Research Notices publication_status: published publisher: Oxford University Press publist_id: '7749' quality_controlled: '1' status: public title: Strong approximation and a conjecture of Harpaz and Wittenberg type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '391' abstract: - lang: eng text: 'Three-dimensional topological insulators are bulk insulators with Z 2 topological electronic order that gives rise to conducting light-like surface states. These surface electrons are exceptionally resistant to localization by non-magnetic disorder, and have been adopted as the basis for a wide range of proposals to achieve new quasiparticle species and device functionality. Recent studies have yielded a surprise by showing that in spite of resisting localization, topological insulator surface electrons can be reshaped by defects into distinctive resonance states. Here we use numerical simulations and scanning tunnelling microscopy data to show that these resonance states have significance well beyond the localized regime usually associated with impurity bands. At native densities in the model Bi2X3 (X=Bi, Te) compounds, defect resonance states are predicted to generate a new quantum basis for an emergent electron gas that supports diffusive electrical transport. ' author: - first_name: Yishuai full_name: Xu, Yishuai last_name: Xu - first_name: Janet full_name: Chiu, Janet last_name: Chiu - first_name: Lin full_name: Miao, Lin last_name: Miao - first_name: Haowei full_name: He, Haowei last_name: He - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Aharon full_name: Kapitulnik, Aharon last_name: Kapitulnik - first_name: Rudro full_name: Biswas, Rudro last_name: Biswas - first_name: Lewis full_name: Wray, Lewis last_name: Wray citation: ama: Xu Y, Chiu J, Miao L, et al. Disorder enabled band structure engineering of a topological insulator surface. Nature Communications. 2017;8. doi:10.1038/ncomms14081 apa: Xu, Y., Chiu, J., Miao, L., He, H., Alpichshev, Z., Kapitulnik, A., … Wray, L. (2017). Disorder enabled band structure engineering of a topological insulator surface. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14081 chicago: Xu, Yishuai, Janet Chiu, Lin Miao, Haowei He, Zhanybek Alpichshev, Aharon Kapitulnik, Rudro Biswas, and Lewis Wray. “Disorder Enabled Band Structure Engineering of a Topological Insulator Surface.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14081. ieee: Y. Xu et al., “Disorder enabled band structure engineering of a topological insulator surface,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Xu Y, Chiu J, Miao L, He H, Alpichshev Z, Kapitulnik A, Biswas R, Wray L. 2017. Disorder enabled band structure engineering of a topological insulator surface. Nature Communications. 8. mla: Xu, Yishuai, et al. “Disorder Enabled Band Structure Engineering of a Topological Insulator Surface.” Nature Communications, vol. 8, Nature Publishing Group, 2017, doi:10.1038/ncomms14081. short: Y. Xu, J. Chiu, L. Miao, H. He, Z. Alpichshev, A. Kapitulnik, R. Biswas, L. Wray, Nature Communications 8 (2017). date_created: 2018-12-11T11:46:12Z date_published: 2017-02-03T00:00:00Z date_updated: 2021-01-12T07:53:08Z day: '03' doi: 10.1038/ncomms14081 extern: '1' intvolume: ' 8' language: - iso: eng month: '02' oa_version: None publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '7438' status: public title: Disorder enabled band structure engineering of a topological insulator surface type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '393' abstract: - lang: eng text: 'We use a three-pulse ultrafast optical spectroscopy to study the relaxation processes in a frustrated Mott insulator Na2IrO3. By being able to independently produce the out-of-equilibrium bound states (excitons) of doublons and holons with the first pulse and suppress the underlying antiferromagnetic order with the second one, we were able to elucidate the relaxation mechanism of quasiparticles in this system. By observing the difference in the exciton dynamics in the magnetically ordered and disordered phases we found that the mass of this quasiparticle is mostly determined by its interaction with the surrounding spins. ' acknowledgement: "Z.A. gratefully acknowledges discussions with P. A. Lee and A. Kemper. A conversation with J. Zaanen was instrumental in clarifying the physical picture described in this paper. We would also like to thank A. Kogar for thoroughly reading the manuscript and making valuable comments. This work was supported by Army Research Office Grant No. W911NF-15-1-0128 and Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4540 (time resolved optical spectroscopy), Skoltech, as part of the Skoltech NGP program (theory) and National Science Foundation Grant No. DMR-1265162 (material growth).\r\n\r\n" author: - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Edbert full_name: Sie, Edbert last_name: Sie - first_name: Fahad full_name: Mahmood, Fahad last_name: Mahmood - first_name: Gang full_name: Cao, Gang last_name: Cao - first_name: Nuh full_name: Gedik, Nuh last_name: Gedik citation: ama: Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 2017;96(23). doi:10.1103/PhysRevB.96.235141 apa: Alpichshev, Z., Sie, E., Mahmood, F., Cao, G., & Gedik, N. (2017). Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.235141 chicago: Alpichshev, Zhanybek, Edbert Sie, Fahad Mahmood, Gang Cao, and Nuh Gedik. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.235141. ieee: Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, and N. Gedik, “Origin of the exciton mass in the frustrated Mott insulator Na2IrO3,” Physical Review B, vol. 96, no. 23. American Physical Society, 2017. ista: Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. 2017. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 96(23). mla: Alpichshev, Zhanybek, et al. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B, vol. 96, no. 23, American Physical Society, 2017, doi:10.1103/PhysRevB.96.235141. short: Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, N. Gedik, Physical Review B 96 (2017). date_created: 2018-12-11T11:46:13Z date_published: 2017-12-26T00:00:00Z date_updated: 2021-01-12T07:53:16Z day: '26' doi: 10.1103/PhysRevB.96.235141 extern: '1' intvolume: ' 96' issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: http://dspace.mit.edu/handle/1721.1/114259 month: '12' oa: 1 oa_version: None publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '7436' status: public title: Origin of the exciton mass in the frustrated Mott insulator Na2IrO3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ... --- _id: '392' abstract: - lang: eng text: We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static. acknowledgement: Optical pump-probe work was supported by the Gordon and Betty Moore Foundation's EPiQS initiative through Grant No. GBMF4540. Materials growth and characterization was supported by AFOSR FA95501410332 and NSF DMR1410665. author: - first_name: Inna full_name: Vishik, Inna last_name: Vishik - first_name: Fahad full_name: Mahmood, Fahad last_name: Mahmood - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Nuh full_name: Gedik, Nuh last_name: Gedik - first_name: Joshu full_name: Higgins, Joshu last_name: Higgins - first_name: Richard full_name: Greene, Richard last_name: Greene citation: ama: Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 2017;95(11). doi:10.1103/PhysRevB.95.115125 apa: Vishik, I., Mahmood, F., Alpichshev, Z., Gedik, N., Higgins, J., & Greene, R. (2017). Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.95.115125 chicago: Vishik, Inna, Fahad Mahmood, Zhanybek Alpichshev, Nuh Gedik, Joshu Higgins, and Richard Greene. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.115125. ieee: I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, and R. Greene, “Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ,” Physical Review B, vol. 95, no. 11. American Physical Society, 2017. ista: Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. 2017. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 95(11). mla: Vishik, Inna, et al. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B, vol. 95, no. 11, American Physical Society, 2017, doi:10.1103/PhysRevB.95.115125. short: I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, R. Greene, Physical Review B 95 (2017). date_created: 2018-12-11T11:46:13Z date_published: 2017-03-13T00:00:00Z date_updated: 2021-01-12T07:53:12Z day: '13' doi: 10.1103/PhysRevB.95.115125 extern: '1' intvolume: ' 95' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: http://dspace.mit.edu/handle/1721.1/109835 month: '03' oa: 1 oa_version: None publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '7437' status: public title: Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 95 year: '2017' ... --- _id: '443' abstract: - lang: eng text: Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited. author: - first_name: Rae full_name: Hardie, Rae last_name: Hardie - first_name: Ellen full_name: Van Dam, Ellen last_name: Van Dam - first_name: Mark full_name: Cowley, Mark last_name: Cowley - first_name: Ting full_name: Han, Ting last_name: Han - first_name: Seher full_name: Balaban, Seher last_name: Balaban - first_name: Marina full_name: Pajic, Marina last_name: Pajic - first_name: Mark full_name: Pinese, Mark last_name: Pinese - first_name: Mary full_name: Iconomou, Mary last_name: Iconomou - first_name: Robert full_name: Shearer, Robert last_name: Shearer - first_name: Jessie full_name: Mckenna, Jessie last_name: Mckenna - first_name: David full_name: Miller, David last_name: Miller - first_name: Nicola full_name: Waddell, Nicola last_name: Waddell - first_name: John full_name: Pearson, John last_name: Pearson - first_name: Sean full_name: Grimmond, Sean last_name: Grimmond - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Andrew full_name: Biankin, Andrew last_name: Biankin - first_name: Silas full_name: Villas Boas, Silas last_name: Villas Boas - first_name: Andrew full_name: Hoy, Andrew last_name: Hoy - first_name: Nigel full_name: Turner, Nigel last_name: Turner - first_name: Darren full_name: Saunders, Darren last_name: Saunders citation: ama: Hardie R, Van Dam E, Cowley M, et al. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 2017;5(2). doi:10.1186/s40170-017-0164-1 apa: Hardie, R., Van Dam, E., Cowley, M., Han, T., Balaban, S., Pajic, M., … Saunders, D. (2017). Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. BioMed Central. https://doi.org/10.1186/s40170-017-0164-1 chicago: Hardie, Rae, Ellen Van Dam, Mark Cowley, Ting Han, Seher Balaban, Marina Pajic, Mark Pinese, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism. BioMed Central, 2017. https://doi.org/10.1186/s40170-017-0164-1. ieee: R. Hardie et al., “Mitochondrial mutations and metabolic adaptation in pancreatic cancer,” Cancer & Metabolism, vol. 5, no. 2. BioMed Central, 2017. ista: Hardie R, Van Dam E, Cowley M, Han T, Balaban S, Pajic M, Pinese M, Iconomou M, Shearer R, Mckenna J, Miller D, Waddell N, Pearson J, Grimmond S, Sazanov LA, Biankin A, Villas Boas S, Hoy A, Turner N, Saunders D. 2017. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 5(2). mla: Hardie, Rae, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism, vol. 5, no. 2, BioMed Central, 2017, doi:10.1186/s40170-017-0164-1. short: R. Hardie, E. Van Dam, M. Cowley, T. Han, S. Balaban, M. Pajic, M. Pinese, M. Iconomou, R. Shearer, J. Mckenna, D. Miller, N. Waddell, J. Pearson, S. Grimmond, L.A. Sazanov, A. Biankin, S. Villas Boas, A. Hoy, N. Turner, D. Saunders, Cancer & Metabolism 5 (2017). date_created: 2018-12-11T11:46:30Z date_published: 2017-01-30T00:00:00Z date_updated: 2021-01-12T07:56:55Z day: '30' ddc: - '570' doi: 10.1186/s40170-017-0164-1 extern: '1' file: - access_level: open_access checksum: 337a65786875f64a1fe9fc0ac24767dc content_type: application/pdf creator: dernst date_created: 2019-01-22T08:17:56Z date_updated: 2020-07-14T12:46:29Z file_id: '5868' file_name: 2017_Cancer_Hardie.pdf file_size: 1609174 relation: main_file file_date_updated: 2020-07-14T12:46:29Z has_accepted_license: '1' intvolume: ' 5' issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Cancer & Metabolism publication_status: published publisher: BioMed Central publist_id: '7380' quality_controlled: '1' status: public title: Mitochondrial mutations and metabolic adaptation in pancreatic cancer tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2017' ... --- _id: '444' abstract: - lang: eng text: Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations. author: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025' apa: 'Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025' chicago: 'Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025.' ieee: 'L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.' ista: 'Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59.' mla: 'Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:10.1039/9781788010405-00025.' short: L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59. date_created: 2018-12-11T11:46:30Z date_published: 2017-11-29T00:00:00Z date_updated: 2021-01-12T07:56:59Z day: '29' department: - _id: LeSa doi: 10.1039/9781788010405-00025 editor: - first_name: Mårten full_name: Wikström, Mårten last_name: Wikström language: - iso: eng month: '11' oa_version: None page: 25 - 59 publication: 'Mechanisms of primary energy transduction in biology ' publication_identifier: isbn: - 978-1-78262-865-1 publication_status: published publisher: Royal Society of Chemistry publist_id: '7379' quality_controlled: '1' series_title: 'Mechanisms of Primary Energy Transduction in Biology ' status: public title: 'Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '445' abstract: - lang: eng text: The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase. acknowledgement: |- This research was supported in part by the National Science Foundation under Grant No. NSF PHY11-25915. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant No. GBMF4307. D.A. also acknowledges support by Swiss National Science Foundation. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Dimitry full_name: Abanin, Dimitry A last_name: Abanin citation: ama: Serbyn M, Abanin D. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 2017;96(1). doi:10.1103/PhysRevB.96.014202 apa: Serbyn, M., & Abanin, D. (2017). Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.014202 chicago: Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.014202. ieee: M. Serbyn and D. Abanin, “Loschmidt echo in many body localized phases,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1. American Physical Society, 2017. ista: Serbyn M, Abanin D. 2017. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 96(1). mla: Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1, American Physical Society, 2017, doi:10.1103/PhysRevB.96.014202. short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017). date_created: 2018-12-11T11:46:31Z date_published: 2017-07-12T00:00:00Z date_updated: 2021-01-12T07:57:03Z day: '12' doi: 10.1103/PhysRevB.96.014202 extern: 1 intvolume: ' 96' issue: '1' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1701.07772 month: '07' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '7378' quality_controlled: 0 status: public title: Loschmidt echo in many body localized phases type: journal_article volume: 96 year: '2017' ... --- _id: '452' abstract: - lang: eng text: 'Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. Yet, due to the exceeding difficulty of creating stably spinning objects of asymmetric shape in a manual trial-and-error process, there has been little departure from rotationally symmetric designs. With modern 3D printing technologies, however, we can manufacture shapes of almost unbounded complexity at the press of a button, shifting this design complexity toward computation. In this article, we describe an algorithm to generate designs for spinning objects by optimizing their mass distribution: as input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the interior mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. To create voids inside the model, we represent its volume with an adaptive multiresolution voxelization and optimize the discrete voxel fill values using a continuous, nonlinear formulation. We further optimize for rotational stability by maximizing the dominant principal moment. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance.' acknowledgement: "This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting was supported by the ETH Zurich/Marie Curie COFUND Postdoctoral Fellowship. \r\nFirst and foremost, we would like to thank our editor Steve Marschner for his invaluable feedback. We were fortunate to get further help from Maurizio Nitti for model design, Romain Prévost for Make-It-Stand comparisons, Alexander Sorkine-Hornung, Kaan Yücer, and Changil Kim for video and photo assistance, Ronnie Gänsli for metal casting, Alec Jacobson for the posed Elephant and Armadillo models, and Romain Prévost and Amit Bermano for print preparation. Model sources include: Woven Ring: generated by “Sculpture Generator 1” by Carlo H. Séquin, UC Berkeley; Elephant: De Espona model library, courtesy of Robert Sumner; T-Rex: TurboSquid; Armadillo: Stanford Computer Graphics Laboratory; and Utah Teapot: Martin Newell, University of Utah. " article_processing_charge: No author: - first_name: Moritz full_name: Bächer, Moritz last_name: Bächer - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Emily full_name: Whiting, Emily last_name: Whiting - first_name: Olga full_name: Sorkine Hornung, Olga last_name: Sorkine Hornung citation: ama: 'Bächer M, Bickel B, Whiting E, Sorkine Hornung O. Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. 2017;60(8):92-99. doi:10.1145/3068766' apa: 'Bächer, M., Bickel, B., Whiting, E., & Sorkine Hornung, O. (2017). Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. ACM. https://doi.org/10.1145/3068766' chicago: 'Bächer, Moritz, Bernd Bickel, Emily Whiting, and Olga Sorkine Hornung. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” Communications of the ACM. ACM, 2017. https://doi.org/10.1145/3068766.' ieee: 'M. Bächer, B. Bickel, E. Whiting, and O. Sorkine Hornung, “Spin it: Optimizing moment of inertia for spinnable objects,” Communications of the ACM, vol. 60, no. 8. ACM, pp. 92–99, 2017.' ista: 'Bächer M, Bickel B, Whiting E, Sorkine Hornung O. 2017. Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. 60(8), 92–99.' mla: 'Bächer, Moritz, et al. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” Communications of the ACM, vol. 60, no. 8, ACM, 2017, pp. 92–99, doi:10.1145/3068766.' short: M. Bächer, B. Bickel, E. Whiting, O. Sorkine Hornung, Communications of the ACM 60 (2017) 92–99. date_created: 2018-12-11T11:46:33Z date_published: 2017-08-01T00:00:00Z date_updated: 2022-03-18T12:55:28Z day: '01' doi: 10.1145/3068766 extern: '1' intvolume: ' 60' issue: '8' language: - iso: eng month: '08' oa_version: None page: 92 - 99 publication: Communications of the ACM publication_status: published publisher: ACM publist_id: '7370' scopus_import: '1' status: public title: 'Spin it: Optimizing moment of inertia for spinnable objects' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2017' ... --- _id: '453' abstract: - lang: eng text: Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor. acknowledgement: 'The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ' article_processing_charge: No article_type: original author: - first_name: Todd full_name: Fallesen, Todd last_name: Fallesen - first_name: Johanna full_name: Roostalu, Johanna last_name: Roostalu - first_name: Christian F full_name: Düllberg, Christian F id: 459064DC-F248-11E8-B48F-1D18A9856A87 last_name: Düllberg orcid: 0000-0001-6335-9748 - first_name: Gunnar full_name: Pruessner, Gunnar last_name: Pruessner - first_name: Thomas full_name: Surrey, Thomas last_name: Surrey citation: ama: Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006 apa: Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006 chicago: Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006. ieee: T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017. ista: Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067. mla: Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006. short: T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067. date_created: 2018-12-11T11:46:33Z date_published: 2017-11-07T00:00:00Z date_updated: 2021-01-12T07:59:28Z day: '07' ddc: - '570' department: - _id: MaLo doi: 10.1016/j.bpj.2017.09.006 file: - access_level: open_access checksum: 99a2474088e20ac74b1882c4fbbb45b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:03Z date_updated: 2020-07-14T12:46:31Z file_id: '5052' file_name: IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf file_size: 977192 relation: main_file file_date_updated: 2020-07-14T12:46:31Z has_accepted_license: '1' intvolume: ' 113' issue: '9' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 2055 - 2067 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '7369' pubrep_id: '965' quality_controlled: '1' status: public title: Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2017' ... --- _id: '464' abstract: - lang: eng text: The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years. article_number: '26' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017 apa: Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017 chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017. ieee: K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017. ista: Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26. mla: Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017. short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017). date_created: 2018-12-11T11:46:37Z date_published: 2017-09-26T00:00:00Z date_updated: 2023-02-23T10:08:55Z day: '26' ddc: - '004' department: - _id: KrCh doi: 10.23638/LMCS-13(3:26)2017 ec_funded: 1 external_id: arxiv: - '1410.0833' file: - access_level: open_access checksum: 12d469ae69b80361333d7dead965cf5d content_type: application/pdf creator: system date_created: 2018-12-12T10:13:27Z date_updated: 2020-07-14T12:46:32Z file_id: '5010' file_name: IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf file_size: 582940 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '09' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Logical Methods in Computer Science publication_identifier: issn: - 1860-5974 publication_status: published publisher: International Federation of Computational Logic publist_id: '7357' pubrep_id: '956' quality_controlled: '1' related_material: record: - id: '1661' relation: earlier_version status: public scopus_import: '1' status: public title: Improved algorithms for parity and Streett objectives tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '470' abstract: - lang: eng text: This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios. acknowledged_ssus: - _id: ScienComp article_number: '103' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678 apa: Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678 chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678. ieee: S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017. ista: Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103. mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678. short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017). date_created: 2018-12-11T11:46:39Z date_published: 2017-07-01T00:00:00Z date_updated: 2023-02-23T12:20:26Z day: '01' ddc: - '006' department: - _id: ChWo doi: 10.1145/3072959.3073678 ec_funded: 1 file: - access_level: open_access checksum: 82a3b2bfeee4ddef16ecc21675d1a48a content_type: application/pdf creator: wojtan date_created: 2020-01-24T09:32:35Z date_updated: 2020-07-14T12:46:34Z file_id: '7359' file_name: wavepackets_final.pdf file_size: 13131683 relation: main_file file_date_updated: 2020-07-14T12:46:34Z has_accepted_license: '1' intvolume: ' 36' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: ACM Transactions on Graphics publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '7350' quality_controlled: '1' scopus_import: 1 status: public title: Water wave packets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ... --- _id: '471' abstract: - lang: eng text: 'We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. ' article_number: '12' author: - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 2017;18(2). doi:10.1145/3060139 apa: Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2017). Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3060139 chicago: Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139. ieee: P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2. ACM, 2017. ista: Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 18(2), 12. mla: Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2, 12, ACM, 2017, doi:10.1145/3060139. short: P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017). date_created: 2018-12-11T11:46:39Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-02-21T16:48:11Z day: '01' department: - _id: ToHe doi: 10.1145/3060139 ec_funded: 1 intvolume: ' 18' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.05739 month: '05' oa: 1 oa_version: Submitted Version project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ACM Transactions on Computational Logic (TOCL) publication_identifier: issn: - '15293785' publication_status: published publisher: ACM publist_id: '7349' quality_controlled: '1' related_material: record: - id: '1234' relation: earlier_version status: public scopus_import: 1 status: public title: Faster statistical model checking for unbounded temporal properties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2017' ... --- _id: '472' abstract: - lang: eng text: α-Synuclein is a presynaptic protein the function of which has yet to be identified, but its neuronal content increases in patients of synucleinopa-thies including Parkinson’s disease. Chronic overexpression of α-synuclein reportedly expresses various phenotypes of synaptic dysfunction, but the primary target of its toxicity has not been determined. To investigate this, we acutely loaded human recombinant α-synuclein or its pathological mutants in their monomeric forms into the calyces of Held presynaptic terminals in slices from auditorily mature and immature rats of either sex. Membrane capacitance measurements revealed significant and specific inhibitory effects of WT monomeric α-synuclein on vesicle endocytosis throughout development. However, the α-synuclein A53T mutant affected vesicle endocytosis only at immature calyces, where as the A30P mutant had no effect throughout. The endocytic impairment by WTα-synuclein was rescued by intraterminal coloading of the microtubule (MT) polymerization blocker nocodazole. Furthermore, it was reversibly rescued by presynaptically loaded photostatin-1, a pho-toswitcheable inhibitor of MT polymerization, inalight-wavelength-dependent manner. Incontrast, endocyticinhibition by the A53T mutant at immature calyces was not rescued by nocodazole. Functionally, presynaptically loaded WT α-synuclein had no effect on basal synaptic transmission evoked at a low frequency, but significantly attenuated exocytosis and impaired the fidelity of neurotransmission during prolonged high-frequency stimulation. We conclude that monomeric WTα-synuclein primarily inhibits vesicle endocytosis via MT overassembly, thereby impairing high-frequency neurotransmission. author: - first_name: Kohgaku full_name: Eguchi, Kohgaku id: 2B7846DC-F248-11E8-B48F-1D18A9856A87 last_name: Eguchi orcid: 0000-0002-6170-2546 - first_name: Zachari full_name: Taoufiq, Zachari last_name: Taoufiq - first_name: Oliver full_name: Thorn Seshold, Oliver last_name: Thorn Seshold - first_name: Dirk full_name: Trauner, Dirk last_name: Trauner - first_name: Masato full_name: Hasegawa, Masato last_name: Hasegawa - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 2017;37(25):6043-6052. doi:10.1523/JNEUROSCI.0179-17.2017 apa: Eguchi, K., Taoufiq, Z., Thorn Seshold, O., Trauner, D., Hasegawa, M., & Takahashi, T. (2017). Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1523/JNEUROSCI.0179-17.2017 chicago: Eguchi, Kohgaku, Zachari Taoufiq, Oliver Thorn Seshold, Dirk Trauner, Masato Hasegawa, and Tomoyuki Takahashi. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1523/JNEUROSCI.0179-17.2017. ieee: K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, and T. Takahashi, “Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held,” European Journal of Neuroscience, vol. 37, no. 25. Wiley-Blackwell, pp. 6043–6052, 2017. ista: Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. 2017. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 37(25), 6043–6052. mla: Eguchi, Kohgaku, et al. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience, vol. 37, no. 25, Wiley-Blackwell, 2017, pp. 6043–52, doi:10.1523/JNEUROSCI.0179-17.2017. short: K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, T. Takahashi, European Journal of Neuroscience 37 (2017) 6043–6052. date_created: 2018-12-11T11:46:40Z date_published: 2017-06-21T00:00:00Z date_updated: 2021-01-12T08:00:51Z day: '21' doi: 10.1523/JNEUROSCI.0179-17.2017 extern: '1' intvolume: ' 37' issue: '25' language: - iso: eng month: '06' oa_version: None page: 6043 - 6052 publication: European Journal of Neuroscience publication_identifier: issn: - '02706474' publication_status: published publisher: Wiley-Blackwell publist_id: '7348' quality_controlled: '1' status: public title: Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2017' ... --- _id: '481' abstract: - lang: eng text: We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings. acknowledgement: 'Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.' author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229. doi:10.1142/S0218195916600050 apa: Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195916600050 chicago: Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050. ieee: T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017. ista: Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229. mla: Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050. short: T. Biedl, S. Huber, P. Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229. date_created: 2018-12-11T11:46:43Z date_published: 2017-04-13T00:00:00Z date_updated: 2023-02-21T16:06:22Z day: '13' ddc: - '004' - '514' - '516' department: - _id: HeEd doi: 10.1142/S0218195916600050 file: - access_level: open_access checksum: f79e8558bfe4b368dfefeb8eec2e3a5e content_type: application/pdf creator: system date_created: 2018-12-12T10:09:34Z date_updated: 2020-07-14T12:46:35Z file_id: '4758' file_name: IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf file_size: 769296 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 26' issue: 3-4 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 211 - 229 publication: International Journal of Computational Geometry and Applications publication_status: published publisher: World Scientific Publishing publist_id: '7338' pubrep_id: '949' quality_controlled: '1' related_material: record: - id: '10892' relation: earlier_version status: public scopus_import: 1 status: public title: Planar matchings for weighted straight skeletons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2017' ... --- _id: '484' abstract: - lang: eng text: We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory. author: - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski citation: ama: Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4 apa: Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4 chicago: Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4. ieee: P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017. ista: Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3), 683–738. mla: Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4. short: P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738. date_created: 2018-12-11T11:46:43Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:00:58Z day: '01' department: - _id: RoSe doi: 10.4310/ATMP.2017.v21.n3.a4 ec_funded: 1 intvolume: ' 21' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.04631 month: '01' oa: 1 oa_version: Submitted Version page: 683 - 738 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Advances in Theoretical and Mathematical Physics publication_identifier: issn: - '10950761' publication_status: published publisher: International Press publist_id: '7336' quality_controlled: '1' scopus_import: 1 status: public title: Bogoliubov correction to the mean-field dynamics of interacting bosons type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2017' ... --- _id: '483' abstract: - lang: eng text: We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices. author: - first_name: Paul full_name: Bourgade, Paul last_name: Bourgade - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Horng full_name: Yau, Horng last_name: Yau - first_name: Jun full_name: Yin, Jun last_name: Yin citation: ama: Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5 apa: Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5 chicago: Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5. ieee: P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017. ista: Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800. mla: Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5. short: P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800. date_created: 2018-12-11T11:46:43Z date_published: 2017-08-25T00:00:00Z date_updated: 2021-01-12T08:00:57Z day: '25' department: - _id: LaEr doi: 10.4310/ATMP.2017.v21.n3.a5 ec_funded: 1 intvolume: ' 21' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.02312 month: '08' oa: 1 oa_version: Submitted Version page: 739 - 800 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Advances in Theoretical and Mathematical Physics publication_identifier: issn: - '10950761' publication_status: published publisher: International Press publist_id: '7337' quality_controlled: '1' scopus_import: 1 status: public title: Universality for a class of random band matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2017' ... --- _id: '487' abstract: - lang: eng text: In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x. author: - first_name: Ghufran full_name: Baig, Ghufran last_name: Baig - first_name: Bozidar full_name: Radunovic, Bozidar last_name: Radunovic - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Matthew full_name: Balkwill, Matthew last_name: Balkwill - first_name: Thomas full_name: Karagiannis, Thomas last_name: Karagiannis - first_name: Lili full_name: Qiu, Lili last_name: Qiu citation: ama: 'Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies. ACM; 2017:2-14. doi:10.1145/3143361.3143367' apa: 'Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., & Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367' chicago: Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill, Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV White Spaces.” In Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367. ieee: G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L. Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies, Incheon, South Korea, 2017, pp. 2–14. ista: 'Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017. Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies. CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14.' mla: Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.” Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367. short: G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu, in:, Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14. conference: end_date: 2017-12-15 location: Incheon, South Korea name: 'CoNEXT: Conference on emerging Networking EXperiments and Technologies' start_date: 2017-12-12 date_created: 2018-12-11T11:46:45Z date_published: 2017-11-28T00:00:00Z date_updated: 2023-02-23T12:21:11Z day: '28' department: - _id: DaAl doi: 10.1145/3143361.3143367 language: - iso: eng month: '11' oa_version: None page: 2 - 14 publication: Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies publication_identifier: isbn: - 978-145035422-6 publication_status: published publisher: ACM publist_id: '7333' quality_controlled: '1' scopus_import: 1 status: public title: Towards unlicensed cellular networks in TV white spaces type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '514' abstract: - lang: eng text: 'Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.' article_number: '16032' author: - first_name: Jean full_name: Simonnet, Jean last_name: Simonnet - first_name: Mérie full_name: Nassar, Mérie last_name: Nassar - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Ivan full_name: Cohen, Ivan last_name: Cohen - first_name: Bertrand full_name: Mathon, Bertrand last_name: Mathon - first_name: Charlotte full_name: Boccara, Charlotte id: 3FC06552-F248-11E8-B48F-1D18A9856A87 last_name: Boccara orcid: 0000-0001-7237-5109 - first_name: Richard full_name: Miles, Richard last_name: Miles - first_name: Desdemona full_name: Fricker, Desdemona last_name: Fricker citation: ama: Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032 apa: Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032 chicago: Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032. ieee: J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032. mla: Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032. short: J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017). date_created: 2018-12-11T11:46:54Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:01:16Z day: '01' ddc: - '571' department: - _id: JoCs doi: 10.1038/ncomms16032 file: - access_level: open_access checksum: 76d8a2b72a58e56adb410ec37dfa7eee content_type: application/pdf creator: system date_created: 2018-12-12T10:14:31Z date_updated: 2020-07-14T12:46:36Z file_id: '5083' file_name: IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf file_size: 2948357 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7305' pubrep_id: '937' quality_controlled: '1' scopus_import: 1 status: public title: Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '515' abstract: - lang: eng text: 'The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.' article_type: original author: - first_name: James A full_name: Letts, James A id: 322DA418-F248-11E8-B48F-1D18A9856A87 last_name: Letts orcid: 0000-0002-9864-3586 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460' apa: 'Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460' chicago: 'Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.' ieee: 'J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.' ista: 'Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.' mla: 'Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460.' short: J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808. date_created: 2018-12-11T11:46:54Z date_published: 2017-10-05T00:00:00Z date_updated: 2021-01-12T08:01:17Z day: '05' ddc: - '572' department: - _id: LeSa doi: 10.1038/nsmb.3460 ec_funded: 1 file: - access_level: open_access checksum: 9bc7e8c41b43636dd7566289e511f096 content_type: application/pdf creator: lsazanov date_created: 2019-11-07T12:51:07Z date_updated: 2020-07-14T12:46:36Z file_id: '6993' file_name: 29893_2_merged_1501257589_red.pdf file_size: 4118385 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 24' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 800 - 808 project: - _id: 2590DB08-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '701309' name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020) publication: Nature Structural and Molecular Biology publication_identifier: issn: - '15459993' publication_status: published publisher: Nature Publishing Group publist_id: '7304' quality_controlled: '1' scopus_import: 1 status: public title: 'Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2017' ... --- _id: '513' abstract: - lang: eng text: 'We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction.' article_number: '043904' author: - first_name: Lukasz full_name: Klotz, Lukasz id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87 last_name: Klotz orcid: 0000-0003-1740-7635 - first_name: Grégoire M full_name: Lemoult, Grégoire M id: 4787FE80-F248-11E8-B48F-1D18A9856A87 last_name: Lemoult - first_name: Idalia full_name: Frontczak, Idalia last_name: Frontczak - first_name: Laurette full_name: Tuckerman, Laurette last_name: Tuckerman - first_name: José full_name: Wesfreid, José last_name: Wesfreid citation: ama: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904' apa: 'Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904' chicago: 'Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.' ieee: 'L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.' ista: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904.' mla: 'Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.' short: L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017). date_created: 2018-12-11T11:46:54Z date_published: 2017-04-01T00:00:00Z date_updated: 2021-01-12T08:01:16Z day: '01' department: - _id: BjHo doi: 10.1103/PhysRevFluids.2.043904 intvolume: ' 2' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.02619 month: '04' oa: 1 oa_version: Preprint publication: Physical Review Fluids publication_status: published publisher: American Physical Society publist_id: '7306' quality_controlled: '1' scopus_import: 1 status: public title: 'Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2017' ... --- _id: '520' abstract: - lang: eng text: Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here. article_type: letter_note author: - first_name: Wei full_name: Du, Wei last_name: Du - first_name: Andreas full_name: Angermayr, Andreas id: 4677C796-F248-11E8-B48F-1D18A9856A87 last_name: Angermayr orcid: 0000-0001-8619-2223 - first_name: Joeri full_name: Jongbloets, Joeri last_name: Jongbloets - first_name: Douwe full_name: Molenaar, Douwe last_name: Molenaar - first_name: Herwig full_name: Bachmann, Herwig last_name: Bachmann - first_name: Klaas full_name: Hellingwerf, Klaas last_name: Hellingwerf - first_name: Filipe full_name: Branco Dos Santos, Filipe last_name: Branco Dos Santos citation: ama: Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235 apa: Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235 chicago: Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235. ieee: W. Du et al., “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” ACS Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017. ista: Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401. mla: Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235. short: W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401. date_created: 2018-12-11T11:46:56Z date_published: 2017-03-17T00:00:00Z date_updated: 2021-01-12T08:01:21Z day: '17' department: - _id: ToBo doi: 10.1021/acssynbio.6b00235 external_id: pmid: - '27936615' intvolume: ' 6' issue: '3' language: - iso: eng month: '03' oa_version: None page: 395 - 401 pmid: 1 publication: ACS Synthetic Biology publication_identifier: issn: - '21615063' publication_status: published publisher: American Chemical Society publist_id: '7298' quality_controlled: '1' scopus_import: 1 status: public title: Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2017' ... --- _id: '521' abstract: - lang: eng text: Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension. author: - first_name: Kyle full_name: Austin, Kyle last_name: Austin - first_name: Ziga full_name: Virk, Ziga id: 2E36B656-F248-11E8-B48F-1D18A9856A87 last_name: Virk citation: ama: Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005 apa: Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005 chicago: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005. ieee: K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017. ista: Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57. mla: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005. short: K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57. date_created: 2018-12-11T11:46:56Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:01:21Z day: '01' department: - _id: HeEd doi: 10.1016/j.topol.2016.10.005 intvolume: ' 215' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.03954v1 month: '01' oa: 1 oa_version: Submitted Version page: 45 - 57 publication: Topology and its Applications publication_identifier: issn: - '01668641' publication_status: published publisher: Elsevier publist_id: '7299' quality_controlled: '1' status: public title: Higson compactification and dimension raising type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 215 year: '2017' ... --- _id: '525' abstract: - lang: eng text: 'The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity. ' acknowledgement: "Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1 and BB/H020314/1\t" author: - first_name: Daniel full_name: Daniel von Wangenheim id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Tatsuaki full_name: Goh, Tatsuaki last_name: Goh - first_name: Daniela full_name: Dietrich, Daniela last_name: Dietrich - first_name: Malcolm full_name: Bennett, Malcolm J last_name: Bennett citation: ama: 'von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers… in roots. Current Biology. 2017;27(5):R172-R174. doi:10.1016/j.cub.2017.01.060' apa: 'von Wangenheim, D., Goh, T., Dietrich, D., & Bennett, M. (2017). Plant biology: Building barriers… in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.01.060' chicago: 'Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett. “Plant Biology: Building Barriers… in Roots.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.01.060.' ieee: 'D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building barriers… in roots,” Current Biology, vol. 27, no. 5. Cell Press, pp. R172–R174, 2017.' ista: 'von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building barriers… in roots. Current Biology. 27(5), R172–R174.' mla: 'von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.” Current Biology, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:10.1016/j.cub.2017.01.060.' short: D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017) R172–R174. date_created: 2018-12-11T11:46:58Z date_published: 2017-03-06T00:00:00Z date_updated: 2021-01-12T08:01:23Z day: '06' doi: 10.1016/j.cub.2017.01.060 extern: 1 file: - access_level: open_access checksum: 81fd4475c5a2a2c6f4313beeab215ed9 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:11Z date_updated: 2020-07-14T12:46:38Z file_id: '5330' file_name: IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf file_size: 2840413 relation: main_file file_date_updated: 2020-07-14T12:46:38Z intvolume: ' 27' issue: '5' main_file_link: - open_access: '1' url: https://repository.ist.ac.at/id/eprint/983 month: '03' oa: 1 page: R172 - R174 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '7294' pubrep_id: '983' quality_controlled: 0 status: public title: 'Plant biology: Building barriers… in roots' type: journal_article volume: 27 year: '2017' ... --- _id: '529' abstract: - lang: eng text: The pituitary adenylyl cyclase-activating polypeptide (PACAP) and its G protein-coupled receptors, PAC1, VPAC1 and VPAC2 form a system involved in a variety of biological processes. Although some sympathetic stimulatory effects of this system have been reported, its central cardiovascular regulatory properties are poorly characterized. VPAC1 receptors are expressed in the nucleus ambiguus (nAmb), a key center controlling cardiac parasympathetic tone. In this study, we report that selective VPAC1 activation in rhodamine-labeled cardiac vagal preganglionic neurons of the rat nAmb produces inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization, membrane depolarization and activation of P/Q-type Ca2+ channels. In vivo, this pathway converges onto transient reduction in heart rate of conscious rats. Therefore we demonstrate a VPAC1-dependent mechanism in the central parasympathetic regulation of the heart rate, adding to the complexity of PACAP-mediated cardiovascular modulation. acknowledgement: This study was supported by startup funds from the Jefferson College of Pharmacy, and by the National Institutes of Health DA023204 (to M.E.A) and P30 DA 013429 to Center for Substance Abuse Research, Temple University. author: - first_name: Florin full_name: Gherghina, Florin L last_name: Gherghina - first_name: Andrei full_name: Tica, Andrei A last_name: Tica - first_name: Elena full_name: Elena Deliu id: 37A40D7E-F248-11E8-B48F-1D18A9856A87 last_name: Deliu orcid: 0000-0002-7370-5293 - first_name: Mary full_name: Abood, Mary E last_name: Abood - first_name: G. full_name: Brailoiu, G. Christina last_name: Brailoiu - first_name: Eugen full_name: Brǎiloiu, Eugen last_name: Brǎiloiu citation: ama: Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 2017;1657:297-303. doi:10.1016/j.brainres.2016.12.026 apa: Gherghina, F., Tica, A., Deliu, E., Abood, M., Brailoiu, G., & Brǎiloiu, E. (2017). Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. Elsevier. https://doi.org/10.1016/j.brainres.2016.12.026 chicago: Gherghina, Florin, Andrei Tica, Elena Deliu, Mary Abood, G. Brailoiu, and Eugen Brǎiloiu. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain Research. Elsevier, 2017. https://doi.org/10.1016/j.brainres.2016.12.026. ieee: F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, and E. Brǎiloiu, “Effects of VPAC1 activation in nucleus ambiguus neurons,” Brain Research, vol. 1657. Elsevier, pp. 297–303, 2017. ista: Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. 2017. Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 1657, 297–303. mla: Gherghina, Florin, et al. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain Research, vol. 1657, Elsevier, 2017, pp. 297–303, doi:10.1016/j.brainres.2016.12.026. short: F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, E. Brǎiloiu, Brain Research 1657 (2017) 297–303. date_created: 2018-12-11T11:46:59Z date_published: 2017-02-15T00:00:00Z date_updated: 2021-01-12T08:01:26Z day: '15' doi: 10.1016/j.brainres.2016.12.026 extern: 1 intvolume: ' 1657' month: '02' page: 297 - 303 publication: Brain Research publication_status: published publisher: Elsevier publist_id: '7290' quality_controlled: 0 status: public title: Effects of VPAC1 activation in nucleus ambiguus neurons type: journal_article volume: 1657 year: '2017' ... --- _id: '534' abstract: - lang: eng text: We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case. article_processing_charge: No article_type: original author: - first_name: Benjamin full_name: Burton, Benjamin last_name: Burton - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0 apa: Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0 chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0. ieee: B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017. ista: Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888. mla: Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0. short: B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888. date_created: 2018-12-11T11:47:01Z date_published: 2017-06-09T00:00:00Z date_updated: 2023-02-21T17:01:34Z day: '09' department: - _id: UlWa doi: 10.1007/s00454-017-9900-0 external_id: arxiv: - '1602.07907' intvolume: ' 58' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.07907 month: '06' oa: 1 oa_version: Preprint page: 871 - 888 publication: Discrete & Computational Geometry publication_identifier: issn: - '01795376' publication_status: published publisher: Springer publist_id: '7283' quality_controlled: '1' related_material: record: - id: '1379' relation: earlier_version status: public scopus_import: 1 status: public title: Finding non-orientable surfaces in 3-Manifolds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2017' ... --- _id: '538' abstract: - lang: ger text: 'Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. ' author: - first_name: Stephanie full_name: Kainrath, Stephanie id: 32CFBA64-F248-11E8-B48F-1D18A9856A87 last_name: Kainrath - first_name: Manuela full_name: Stadler, Manuela last_name: Stadler - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 - first_name: Martin full_name: Distel, Martin last_name: Distel - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998 apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998 chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998. ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017. ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682. mla: Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998. short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682. date_created: 2018-12-11T11:47:02Z date_published: 2017-05-20T00:00:00Z date_updated: 2021-01-12T08:01:33Z day: '20' ddc: - '571' department: - _id: CaGu - _id: HaJa doi: 10.1002/ange.201611998 ec_funded: 1 file: - access_level: open_access checksum: d66fee867e7cdbfa3fe276c2fb0778bb content_type: application/pdf creator: system date_created: 2018-12-12T10:13:24Z date_updated: 2020-07-14T12:46:39Z file_id: '5007' file_name: IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf file_size: 1668557 relation: main_file file_date_updated: 2020-07-14T12:46:39Z has_accepted_license: '1' intvolume: ' 129' issue: '16' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 4679 - 4682 project: - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology - _id: 255A6082-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Angewandte Chemie publication_status: published publisher: Wiley publist_id: '7279' pubrep_id: '932' quality_controlled: '1' status: public title: Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2017' ... --- _id: '540' abstract: - lang: eng text: RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host. article_number: e1006758 author: - first_name: Kseniya full_name: Khamina, Kseniya last_name: Khamina - first_name: Alexander full_name: Lercher, Alexander last_name: Lercher - first_name: Michael full_name: Caldera, Michael last_name: Caldera - first_name: Christopher full_name: Schliehe, Christopher last_name: Schliehe - first_name: Bojan full_name: Vilagos, Bojan last_name: Vilagos - first_name: Mehmet full_name: Sahin, Mehmet last_name: Sahin - first_name: Lindsay full_name: Kosack, Lindsay last_name: Kosack - first_name: Anannya full_name: Bhattacharya, Anannya last_name: Bhattacharya - first_name: Peter full_name: Májek, Peter last_name: Májek - first_name: Alexey full_name: Stukalov, Alexey last_name: Stukalov - first_name: Roberto full_name: Sacco, Roberto id: 42C9F57E-F248-11E8-B48F-1D18A9856A87 last_name: Sacco - first_name: Leo full_name: James, Leo last_name: James - first_name: Daniel full_name: Pinschewer, Daniel last_name: Pinschewer - first_name: Keiryn full_name: Bennett, Keiryn last_name: Bennett - first_name: Jörg full_name: Menche, Jörg last_name: Menche - first_name: Andreas full_name: Bergthaler, Andreas last_name: Bergthaler citation: ama: Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758 apa: Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758 chicago: Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758. ieee: K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017. ista: Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758. mla: Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758. short: K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017). date_created: 2018-12-11T11:47:03Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:01:48Z day: '01' ddc: - '576' - '616' department: - _id: GaNo doi: 10.1371/journal.ppat.1006758 file: - access_level: open_access checksum: 1aa20f19a1e90664fadce6e7d5284fdc content_type: application/pdf creator: system date_created: 2018-12-12T10:12:26Z date_updated: 2020-07-14T12:46:44Z file_id: '4944' file_name: IST-2018-931-v1+1_journal.ppat.1006758.pdf file_size: 4106772 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' intvolume: ' 13' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: PLoS Pathogens publication_identifier: issn: - '15537366' publication_status: published publisher: Public Library of Science publist_id: '7276' pubrep_id: '931' quality_controlled: '1' scopus_import: 1 status: public title: Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '466' abstract: - lang: eng text: 'We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. ' article_number: '15' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Křetínská, Zuzana last_name: Křetínská - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017 apa: Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017 chicago: Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017. ieee: K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017. ista: Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15. mla: Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017. short: K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017). date_created: 2018-12-11T11:46:38Z date_published: 2017-07-03T00:00:00Z date_updated: 2023-02-23T12:26:16Z day: '03' ddc: - '004' department: - _id: KrCh doi: 10.23638/LMCS-13(2:15)2017 ec_funded: 1 file: - access_level: open_access checksum: bfa405385ec6229ad5ead89ab5751639 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:32Z date_updated: 2020-07-14T12:46:33Z file_id: '5354' file_name: IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf file_size: 511832 relation: main_file file_date_updated: 2020-07-14T12:46:33Z has_accepted_license: '1' intvolume: ' 13' issue: '2' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2590DB08-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '701309' name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020) publication: Logical Methods in Computer Science publication_identifier: issn: - '18605974' publication_status: published publisher: International Federation of Computational Logic publist_id: '7355' pubrep_id: '957' quality_controlled: '1' related_material: record: - id: '1657' relation: earlier_version status: public - id: '5429' relation: earlier_version status: public - id: '5435' relation: earlier_version status: public scopus_import: 1 status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '467' abstract: - lang: eng text: Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties. article_number: '31' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769 apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017. ista: Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31. mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769. short: K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017). date_created: 2018-12-11T11:46:38Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-02-23T12:26:19Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1145/3152769 ec_funded: 1 external_id: arxiv: - '1606.03598' intvolume: ' 18' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.03598 month: '12' oa: 1 oa_version: Preprint project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _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 publication: ACM Transactions on Computational Logic (TOCL) publication_identifier: issn: - '15293785' publication_status: published publisher: ACM publist_id: '7354' quality_controlled: '1' related_material: record: - id: '1656' relation: earlier_version status: public - id: '5415' relation: earlier_version status: public - id: '5436' relation: earlier_version status: public scopus_import: 1 status: public title: Nested weighted automata type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2017' ... --- _id: '465' abstract: - lang: eng text: 'The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Jan full_name: Otop, Jan last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017 apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017. ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017. ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3). mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017. short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017). date_created: 2018-12-11T11:46:37Z date_published: 2017-09-13T00:00:00Z date_updated: 2023-02-23T12:26:25Z day: '13' ddc: - '004' department: - _id: KrCh - _id: ToHe doi: 10.23638/LMCS-13(3:23)2017 ec_funded: 1 file: - access_level: open_access checksum: 08041379ba408d40664f449eb5907a8f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:37Z date_updated: 2020-07-14T12:46:33Z file_id: '5090' file_name: IST-2015-321-v1+1_main.pdf file_size: 279071 relation: main_file - access_level: open_access checksum: 08041379ba408d40664f449eb5907a8f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:38Z date_updated: 2020-07-14T12:46:33Z file_id: '5091' file_name: IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf file_size: 279071 relation: main_file file_date_updated: 2020-07-14T12:46:33Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Logical Methods in Computer Science publication_identifier: issn: - '18605974' publication_status: published publisher: International Federation of Computational Logic publist_id: '7356' pubrep_id: '955' quality_controlled: '1' related_material: record: - id: '1610' relation: earlier_version status: public - id: '5438' relation: earlier_version status: public scopus_import: 1 status: public title: Edit distance for pushdown automata tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '512' abstract: - lang: eng text: 'The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. ' article_number: '82' article_processing_charge: No author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-00107-w' apa: 'Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w' chicago: 'Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.' ieee: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 2017.' ista: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.' mla: 'Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w.' short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017). date_created: 2018-12-11T11:46:53Z date_published: 2017-03-06T00:00:00Z date_updated: 2023-02-23T12:26:57Z day: '06' ddc: - '004' department: - _id: KrCh doi: 10.1038/s41598-017-00107-w ec_funded: 1 file: - access_level: open_access checksum: 7d05cbdd914e194a019c0f91fb64e9a8 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:35Z date_updated: 2020-07-14T12:46:36Z file_id: '5357' file_name: IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf file_size: 1536783 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 7' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Scientific Reports publication_identifier: issn: - '20452322' publication_status: published publisher: Nature Publishing Group publist_id: '7307' pubrep_id: '938' quality_controlled: '1' related_material: record: - id: '5449' relation: earlier_version status: public scopus_import: 1 status: public title: 'Amplification on undirected population structures: Comets beat stars' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2017' ... --- _id: '10416' abstract: - lang: eng text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.' acknowledgement: "The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n" article_number: '30' article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Bhavya full_name: Choudhary, Bhavya last_name: Choudhary - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118 apa: 'Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118' chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118. ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017. ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30. mla: Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118. short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017). conference: end_date: 2018-01-13 location: Los Angeles, CA, United States name: 'POPL: Programming Languages' start_date: 2018-01-07 date_created: 2021-12-05T23:01:48Z date_published: 2017-12-27T00:00:00Z date_updated: 2023-02-23T12:27:13Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.1145/3158118 ec_funded: 1 external_id: arxiv: - '1910.00241' file: - access_level: open_access checksum: faa3f7b3fe8aab84b50ed805c26a0ee5 content_type: application/pdf creator: cchlebak date_created: 2021-12-07T08:06:28Z date_updated: 2021-12-07T08:06:28Z file_id: '10421' file_name: 2017_ACMProgLang_Chatterjee.pdf file_size: 460188 relation: main_file success: 1 file_date_updated: 2021-12-07T08:06:28Z has_accepted_license: '1' intvolume: ' 2' issue: POPL language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the ACM on Programming Languages publication_identifier: eissn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '5455' relation: earlier_version status: public scopus_import: '1' status: public title: Optimal Dyck reachability for data-dependence and Alias analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 2 year: '2017' ... --- _id: '5455' abstract: - lang: eng text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks.' alternative_title: - IST Austria Technical Report article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Bhavya full_name: Choudhary, Bhavya last_name: Choudhary - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1 apa: Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1 chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1. ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017. ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p. mla: Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1. short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017. date_created: 2018-12-12T11:39:26Z date_published: 2017-10-23T00:00:00Z date_updated: 2023-02-21T15:54:10Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2017-870-v1-1 file: - access_level: open_access checksum: 177a84a46e3ac17e87b31534ad16a4c9 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:02Z date_updated: 2020-07-14T12:46:59Z file_id: '5524' file_name: IST-2017-870-v1+1_main.pdf file_size: 960491 relation: main_file file_date_updated: 2020-07-14T12:46:59Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '37' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '870' related_material: record: - id: '10416' relation: later_version status: public status: public title: Optimal Dyck reachability for data-dependence and alias analysis type: technical_report user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2017' ... --- _id: '5450' abstract: - lang: eng text: 'In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.' author: - first_name: Barbara full_name: Barbara Petritsch id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 citation: ama: Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017. apa: Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria. chicago: Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017. ieee: B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017. ista: Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p. mla: Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017. short: B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017. date_created: 2018-12-12T11:39:24Z date_published: 2017-06-26T00:00:00Z date_updated: 2020-07-14T23:05:03Z day: '26' department: - _id: E-Lib extern: 0 file: - access_level: open_access checksum: 6321792dcfa82bf490f17615a9b22355 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:22Z date_updated: 2020-07-14T12:46:59Z file_id: '5483' file_name: IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf file_size: 3460985 relation: main_file file_date_updated: 2020-07-14T12:46:59Z main_file_link: - open_access: '1' url: https://repository.ist.ac.at/id/eprint/724. month: '06' oa: 1 publication_date: 2017-06-26 publisher: IST Austria pubrep_id: '724' status: public title: Implementing the institutional data repository IST DataRep type: report year: '2017' ... --- _id: '10417' abstract: - lang: eng text: "We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence." acknowledgement: "The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061." article_number: '31' article_processing_charge: No article_type: original author: - first_name: Marek full_name: Chalupa, Marek last_name: Chalupa - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Nishant full_name: Sinha, Nishant last_name: Sinha - first_name: Kapil full_name: Vaidya, Kapil last_name: Vaidya citation: ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119 apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119' chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119. ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017. ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31. mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119. short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017). conference: end_date: 2018-01-13 location: Los Angeles, CA, United States name: 'POPL: Programming Languages' start_date: 2018-01-07 date_created: 2021-12-05T23:01:49Z date_published: 2017-12-27T00:00:00Z date_updated: 2023-02-23T12:27:16Z day: '27' department: - _id: KrCh doi: 10.1145/3158119 ec_funded: 1 external_id: arxiv: - '1610.01188' intvolume: ' 2' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/doi/10.1145/3158119 month: '12' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the ACM on Programming Languages publication_identifier: eissn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '5448' relation: earlier_version status: public - id: '5456' relation: earlier_version status: public scopus_import: '1' status: public title: Data-centric dynamic partial order reduction type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 2 year: '2017' ... --- _id: '5456' abstract: - lang: eng text: "We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes." alternative_title: - IST Austria Technical Report author: - first_name: Marek full_name: Chalupa, Marek last_name: Chalupa - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Nishant full_name: Sinha, Nishant last_name: Sinha - first_name: Kapil full_name: Vaidya, Kapil last_name: Vaidya citation: ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1 apa: Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1 chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1. ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017. ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p. mla: Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1. short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017. date_created: 2018-12-12T11:39:26Z date_published: 2017-10-23T00:00:00Z date_updated: 2023-02-23T12:26:54Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2017-872-v1-1 file: - access_level: open_access checksum: d2635c4cf013000f0a1b09e80f9e4ab7 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:26Z date_updated: 2020-07-14T12:46:59Z file_id: '5487' file_name: IST-2017-872-v1+1_main.pdf file_size: 910347 relation: main_file file_date_updated: 2020-07-14T12:46:59Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '36' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '872' related_material: record: - id: '10417' relation: later_version status: public - id: '5448' relation: earlier_version status: public status: public title: Data-centric dynamic partial order reduction type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '551' abstract: - lang: eng text: 'Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. ' alternative_title: - LIPIcs article_number: '61' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: 'Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61' apa: 'Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61' chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61. ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83. ista: 'Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 61.' mla: Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” Leibniz International Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61. short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:47:08Z date_published: 2017-11-01T00:00:00Z date_updated: 2021-01-12T08:02:34Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.MFCS.2017.61 file: - access_level: open_access checksum: 2eed5224c0e4e259484a1d71acb8ba6a content_type: application/pdf creator: system date_created: 2018-12-12T10:18:04Z date_updated: 2020-07-14T12:47:00Z file_id: '5322' file_name: IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf file_size: 535077 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Leibniz International Proceedings in Informatics publication_identifier: isbn: - 978-395977046-0 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7263' pubrep_id: '924' quality_controlled: '1' scopus_import: 1 status: public title: Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '552' abstract: - lang: eng text: 'Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).' alternative_title: - LIPIcs article_number: '39' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Svozil, Alexander last_name: Svozil citation: ama: 'Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39' apa: 'Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.39' chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39. ieee: K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83. ista: 'Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.' mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39. short: K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:47:08Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-02-14T10:06:46Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.MFCS.2017.39 ec_funded: 1 file: - access_level: open_access checksum: c67f4866ddbfd555afef1f63ae9a8fc7 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:57Z date_updated: 2020-07-14T12:47:00Z file_id: '5248' file_name: IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf file_size: 610339 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Leibniz International Proceedings in Informatics publication_identifier: isbn: - 978-395977046-0 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7262' pubrep_id: '923' quality_controlled: '1' scopus_import: '1' status: public title: Faster algorithms for mean-payoff parity games tmp: 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) short: CC BY (3.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '553' abstract: - lang: eng text: 'We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. ' alternative_title: - LIPIcs article_number: '55' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Kristofer full_name: Hansen, Kristofer last_name: Hansen - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 citation: ama: 'Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55' apa: 'Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.55' chicago: Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55. ieee: K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83. ista: 'Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.' mla: Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55. short: K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:47:08Z date_published: 2017-11-01T00:00:00Z date_updated: 2021-01-12T08:02:35Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.MFCS.2017.55 file: - access_level: open_access checksum: 7101facb56ade363205c695d72dbd173 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:29Z date_updated: 2020-07-14T12:47:00Z file_id: '4753' file_name: IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf file_size: 549967 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1506.02434 month: '11' oa: 1 oa_version: Published Version publication: Leibniz International Proceedings in Informatics publication_identifier: isbn: - 978-395977046-0 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7261' pubrep_id: '922' quality_controlled: '1' scopus_import: 1 status: public title: Strategy complexity of concurrent safety games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '560' abstract: - lang: eng text: In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions. article_number: '0104' author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Arnulf full_name: Jentzen, Arnulf last_name: Jentzen - first_name: Diyora full_name: Salimova, Diyora last_name: Salimova citation: ama: 'Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104' apa: 'Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104' chicago: 'Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.' ieee: 'M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.' ista: 'Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.' mla: 'Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.' short: 'M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017).' date_created: 2018-12-11T11:47:11Z date_published: 2017-11-01T00:00:00Z date_updated: 2021-01-12T08:03:04Z day: '01' department: - _id: JaMa doi: 10.1098/rspa.2017.0104 ec_funded: 1 intvolume: ' 473' issue: '2207' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.03229 month: '11' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences' publication_identifier: issn: - '13645021' publication_status: published publisher: Royal Society of London publist_id: '7256' quality_controlled: '1' scopus_import: 1 status: public title: On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 473 year: '2017' ... --- _id: '567' abstract: - lang: eng text: "This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n" alternative_title: - Courant Lecture Notes article_processing_charge: No author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Horng full_name: Yau, Horng last_name: Yau citation: ama: Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28. American Mathematical Society; 2017. doi:10.1090/cln/028 apa: Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory (Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028 chicago: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. https://doi.org/10.1090/cln/028. ieee: L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory, vol. 28. American Mathematical Society, 2017. ista: Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p. mla: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028. short: L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017. date_created: 2018-12-11T11:47:13Z date_published: 2017-01-01T00:00:00Z date_updated: 2022-05-24T06:57:28Z day: '01' department: - _id: LaEr doi: 10.1090/cln/028 ec_funded: 1 intvolume: ' 28' language: - iso: eng month: '01' oa_version: None page: '226' project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication_identifier: eisbn: - 978-1-4704-4194-4 isbn: - 9-781-4704-3648-3 publication_status: published publisher: American Mathematical Society publist_id: '7247' quality_controlled: '1' series_title: Courant Lecture Notes status: public title: A Dynamical Approach to Random Matrix Theory type: book user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2017' ... --- _id: '568' abstract: - lang: eng text: 'We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).' author: - first_name: Peter full_name: Franek, Peter id: 473294AE-F248-11E8-B48F-1D18A9856A87 last_name: Franek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál citation: ama: Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16 apa: Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16 chicago: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16. ieee: P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017. ista: Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342. mla: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16. short: P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342. date_created: 2018-12-11T11:47:14Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:03:12Z day: '01' department: - _id: UlWa - _id: HeEd doi: 10.4310/HHA.2017.v19.n2.a16 ec_funded: 1 intvolume: ' 19' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.04310 month: '01' oa: 1 oa_version: Submitted Version page: 313 - 342 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2590DB08-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '701309' name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020) publication: Homology, Homotopy and Applications publication_identifier: issn: - '15320073' publication_status: published publisher: International Press publist_id: '7246' quality_controlled: '1' scopus_import: 1 status: public title: Persistence of zero sets type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '570' abstract: - lang: eng text: 'Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ' article_number: e28921 author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Srdjan full_name: Sarikas, Srdjan id: 35F0286E-F248-11E8-B48F-1D18A9856A87 last_name: Sarikas - first_name: Hande full_name: Acar, Hande id: 2DDF136A-F248-11E8-B48F-1D18A9856A87 last_name: Acar orcid: 0000-0003-1986-9753 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921 apa: Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921 chicago: Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921. ieee: M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921. mla: Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921. short: M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017). date_created: 2018-12-11T11:47:14Z date_published: 2017-11-13T00:00:00Z date_updated: 2021-01-12T08:03:15Z day: '13' ddc: - '576' department: - _id: CaGu - _id: JoBo - _id: NiBa doi: 10.7554/eLife.28921 ec_funded: 1 file: - access_level: open_access checksum: 273ab17f33305e4eaafd911ff88e7c5b content_type: application/pdf creator: system date_created: 2018-12-12T10:14:42Z date_updated: 2020-07-14T12:47:10Z file_id: '5096' file_name: IST-2017-918-v1+1_elife-28921-figures-v3.pdf file_size: 8453470 relation: main_file - access_level: open_access checksum: b433f90576c7be597cd43367946f8e7f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:43Z date_updated: 2020-07-14T12:47:10Z file_id: '5097' file_name: IST-2017-918-v1+2_elife-28921-v3.pdf file_size: 1953221 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '7244' pubrep_id: '918' quality_controlled: '1' scopus_import: 1 status: public title: Regulatory network structure determines patterns of intermolecular epistasis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2017' ... --- _id: '569' abstract: - lang: eng text: The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings. article_number: e30867 author: - first_name: Felix full_name: Spira, Felix last_name: Spira - first_name: Sara full_name: Cuylen Haering, Sara last_name: Cuylen Haering - first_name: Shalin full_name: Mehta, Shalin last_name: Mehta - first_name: Matthias full_name: Samwer, Matthias last_name: Samwer - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Amitabh full_name: Verma, Amitabh last_name: Verma - first_name: Rudolf full_name: Oldenbourg, Rudolf last_name: Oldenbourg - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Daniel full_name: Gerlich, Daniel last_name: Gerlich citation: ama: Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867 apa: Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867 chicago: Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867. ieee: F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867. mla: Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867. short: F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017). date_created: 2018-12-11T11:47:14Z date_published: 2017-11-06T00:00:00Z date_updated: 2023-02-23T12:30:29Z day: '06' ddc: - '570' department: - _id: MiSi doi: 10.7554/eLife.30867 file: - access_level: open_access checksum: ba09c1451153d39e4f4b7cee013e314c content_type: application/pdf creator: system date_created: 2018-12-12T10:10:40Z date_updated: 2020-07-14T12:47:10Z file_id: '4829' file_name: IST-2017-919-v1+1_elife-30867-figures-v1.pdf file_size: 9666973 relation: main_file - access_level: open_access checksum: 01eb51f1d6ad679947415a51c988e137 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:41Z date_updated: 2020-07-14T12:47:10Z file_id: '4830' file_name: IST-2017-919-v1+2_elife-30867-v1.pdf file_size: 5951246 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '7245' pubrep_id: '919' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2017' ... --- _id: '571' abstract: - lang: eng text: Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface. author: - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Zerkah full_name: Ahmad, Zerkah last_name: Ahmad - first_name: Gerhild full_name: Rosenberger, Gerhild last_name: Rosenberger - first_name: Shuxia full_name: Fan, Shuxia last_name: Fan - first_name: Leo full_name: Nicolai, Leo last_name: Nicolai - first_name: Benjamin full_name: Busch, Benjamin last_name: Busch - first_name: Gökce full_name: Yavuz, Gökce last_name: Yavuz - first_name: Manja full_name: Luckner, Manja last_name: Luckner - first_name: Hellen full_name: Ishikawa Ankerhold, Hellen last_name: Ishikawa Ankerhold - first_name: Roman full_name: Hennel, Roman last_name: Hennel - first_name: Alexandre full_name: Benechet, Alexandre last_name: Benechet - first_name: Michael full_name: Lorenz, Michael last_name: Lorenz - first_name: Sue full_name: Chandraratne, Sue last_name: Chandraratne - first_name: Irene full_name: Schubert, Irene last_name: Schubert - first_name: Sebastian full_name: Helmer, Sebastian last_name: Helmer - first_name: Bianca full_name: Striednig, Bianca last_name: Striednig - first_name: Konstantin full_name: Stark, Konstantin last_name: Stark - first_name: Marek full_name: Janko, Marek last_name: Janko - first_name: Ralph full_name: Böttcher, Ralph last_name: Böttcher - first_name: Admar full_name: Verschoor, Admar last_name: Verschoor - first_name: Catherine full_name: Leon, Catherine last_name: Leon - first_name: Christian full_name: Gachet, Christian last_name: Gachet - first_name: Thomas full_name: Gudermann, Thomas last_name: Gudermann - first_name: Michael full_name: Mederos Y Schnitzler, Michael last_name: Mederos Y Schnitzler - first_name: Zachary full_name: Pincus, Zachary last_name: Pincus - first_name: Matteo full_name: Iannacone, Matteo last_name: Iannacone - first_name: Rainer full_name: Haas, Rainer last_name: Haas - first_name: Gerhard full_name: Wanner, Gerhard last_name: Wanner - first_name: Kirsten full_name: Lauber, Kirsten last_name: Lauber - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg citation: ama: Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382. doi:10.1016/j.cell.2017.11.001 apa: Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B., … Massberg, S. (2017). Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001 chicago: Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.11.001. ieee: F. R. Gärtner et al., “Migrating platelets are mechano scavengers that collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press, pp. 1368–1382, 2017. ista: Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 171(6), 1368–1382. mla: Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press, 2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001. short: F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G. Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S. Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher, A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus, M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press 171 (2017) 1368–1382. date_created: 2018-12-11T11:47:15Z date_published: 2017-11-30T00:00:00Z date_updated: 2021-01-12T08:03:15Z day: '30' department: - _id: MiSi doi: 10.1016/j.cell.2017.11.001 ec_funded: 1 intvolume: ' 171' issue: '6' language: - iso: eng month: '11' oa_version: None page: 1368 - 1382 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Cell Press publication_identifier: issn: - '00928674' publication_status: published publisher: Cell Press publist_id: '7243' quality_controlled: '1' scopus_import: 1 status: public title: Migrating platelets are mechano scavengers that collect and bundle bacteria type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 171 year: '2017' ... --- _id: '572' abstract: - lang: eng text: In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture. article_number: '2587' article_processing_charge: No author: - first_name: Damilola full_name: Olatunji, Damilola last_name: Olatunji - first_name: Danny full_name: Geelen, Danny last_name: Geelen - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 citation: ama: Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587 apa: Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587 chicago: Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587. ieee: D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017. ista: Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587. mla: Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587. short: D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017). date_created: 2018-12-11T11:47:15Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:03:16Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.3390/ijms18122587 file: - access_level: open_access checksum: 82d51f11e493f7eec02976d9a9a9805e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:55Z date_updated: 2020-07-14T12:47:10Z file_id: '4718' file_name: IST-2017-917-v1+1_ijms-18-02587.pdf file_size: 920962 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 18' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: International Journal of Molecular Sciences publication_status: published publisher: MDPI publist_id: '7242' pubrep_id: '917' quality_controlled: '1' scopus_import: '1' status: public title: Control of endogenous auxin levels in plant root development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2017' ... --- _id: '5800' abstract: - lang: eng text: This paper presents a novel study on the functional gradation of coordinate planes in connection with the thinnest and tunnel-free (i.e., naive) discretization of sphere in the integer space. For each of the 48-symmetric quadraginta octants of naive sphere with integer radius and integer center, we show that the corresponding voxel set forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as its functional plane. We use this fundamental property to prove several other theoretical results for naive sphere. First, the quadraginta octants form symmetry groups and subgroups with certain equivalent topological properties. Second, a naive sphere is always unique and consists of fewest voxels. Third, it is efficiently constructible from its functional-plane projection. And finally, a special class of 4-symmetric discrete 3D circles can be constructed on a naive sphere based on back projection from the functional plane. author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 2017;59(1):69-83. doi:10.1007/s10851-017-0718-4 apa: Biswas, R., & Bhowmick, P. (2017). On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. Springer Nature. https://doi.org/10.1007/s10851-017-0718-4 chicago: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision. Springer Nature, 2017. https://doi.org/10.1007/s10851-017-0718-4. ieee: R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta octants of naive sphere,” Journal of Mathematical Imaging and Vision, vol. 59, no. 1. Springer Nature, pp. 69–83, 2017. ista: Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83. mla: Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision, vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:10.1007/s10851-017-0718-4. short: R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017) 69–83. date_created: 2019-01-08T20:42:08Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:03:34Z day: '01' doi: 10.1007/s10851-017-0718-4 extern: '1' intvolume: ' 59' issue: '1' language: - iso: eng month: '09' oa_version: None page: 69-83 publication: Journal of Mathematical Imaging and Vision publication_identifier: issn: - '09249907' publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: On the functionality and usefulness of Quadraginta octants of naive sphere type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 59 year: '2017' ... --- _id: '5799' abstract: - lang: eng text: We construct a polyhedral surface called a graceful surface, which provides best possible approximation to a given sphere regarding certain criteria. In digital geometry terms, the graceful surface is uniquely characterized by its minimality while guaranteeing the connectivity of certain discrete (polyhedral) curves defined on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva (1999) and shown to be useful for triangular mesh discretization through graceful planes and graceful lines. In this paper we extend the considerations to a nonlinear object such as a sphere. In particular, we investigate the properties of a discrete geodesic path between two voxels and show that discrete 3D circles, circular arcs, and Mobius triangles are all constructible on a graceful sphere, with guaranteed minimum thickness and the desired connectivity in the discrete topological space. author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick - first_name: Valentin E. full_name: Brimkov, Valentin E. last_name: Brimkov citation: ama: Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 2017;216:362-375. doi:10.1016/j.dam.2015.11.017 apa: Biswas, R., Bhowmick, P., & Brimkov, V. E. (2017). On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2015.11.017 chicago: Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.dam.2015.11.017. ieee: R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres and circular geodesics,” Discrete Applied Mathematics, vol. 216. Elsevier, pp. 362–375, 2017. ista: Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 216, 362–375. mla: Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics, vol. 216, Elsevier, 2017, pp. 362–75, doi:10.1016/j.dam.2015.11.017. short: R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017) 362–375. date_created: 2019-01-08T20:41:12Z date_published: 2017-01-10T00:00:00Z date_updated: 2021-01-12T08:03:33Z day: '10' doi: 10.1016/j.dam.2015.11.017 extern: '1' intvolume: ' 216' language: - iso: eng month: '01' oa_version: None page: 362-375 publication: Discrete Applied Mathematics publication_identifier: issn: - 0166-218X publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: On the polyhedra of graceful spheres and circular geodesics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 216 year: '2017' ... --- _id: '5801' abstract: - lang: eng text: Space filling circles and spheres have various applications in mathematical imaging and physical modeling. In this paper, we first show how the thinnest (i.e., 2-minimal) model of digital sphere can be augmented to a space filling model by fixing certain “simple voxels” and “filler voxels” associated with it. Based on elementary number-theoretic properties of such voxels, we design an efficient incremental algorithm for generation of these space filling spheres with successively increasing radius. The novelty of the proposed technique is established further through circular space filling on 3D digital plane. As evident from a preliminary set of experimental result, this can particularly be useful for parallel computing of 3D Voronoi diagrams in the digital space. alternative_title: - LNCS article_processing_charge: No author: - first_name: Shivam full_name: Dwivedi, Shivam last_name: Dwivedi - first_name: Aniket full_name: Gupta, Aniket last_name: Gupta - first_name: Siddhant full_name: Roy, Siddhant last_name: Roy - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In: 20th IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:347-359. doi:10.1007/978-3-319-66272-5_28' apa: 'Dwivedi, S., Gupta, A., Roy, S., Biswas, R., & Bhowmick, P. (2017). Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In 20th IAPR International Conference (Vol. 10502, pp. 347–359). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_28' chicago: 'Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” In 20th IAPR International Conference, 10502:347–59. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_28.' ieee: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space,” in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502, pp. 347–359. ista: 'Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 347–359.' mla: Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” 20th IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 347–59, doi:10.1007/978-3-319-66272-5_28. short: S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 347–359. conference: end_date: 2017-09-21 location: Vienna, Austria name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery' start_date: 2017-09-19 date_created: 2019-01-08T20:42:22Z date_published: 2017-08-22T00:00:00Z date_updated: 2022-01-27T15:34:25Z day: '22' doi: 10.1007/978-3-319-66272-5_28 extern: '1' intvolume: ' 10502' language: - iso: eng month: '08' oa_version: None page: 347-359 place: Cham publication: 20th IAPR International Conference publication_identifier: eisbn: - 978-3-319-66272-5 eissn: - 1611-3349 isbn: - 978-3-319-66271-8 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 10502 year: '2017' ... --- _id: '5803' abstract: - lang: eng text: Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept. alternative_title: - LNCS article_processing_charge: No author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: 'Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:10.1007/978-3-319-59108-7_8' apa: 'Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256, pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8' chicago: 'Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.' ieee: 'R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.' ista: 'Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.' mla: Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8. short: R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104. conference: end_date: 2017-06-21 location: Plovdiv, Bulgaria name: 'IWCIA: International Workshop on Combinatorial Image Analysis' start_date: 2017-06-19 date_created: 2019-01-08T20:42:56Z date_published: 2017-05-17T00:00:00Z date_updated: 2022-01-28T07:48:24Z day: '17' department: - _id: HeEd doi: 10.1007/978-3-319-59108-7_8 extern: '1' intvolume: ' 10256' language: - iso: eng month: '05' oa_version: None page: 93-104 place: Cham publication: Combinatorial image analysis publication_identifier: isbn: - 978-3-319-59107-0 - 978-3-319-59108-7 issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Construction of persistent Voronoi diagram on 3D digital plane type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 10256 year: '2017' ... --- _id: '5802' abstract: - lang: eng text: This papers introduces a definition of digital primitives based on focal points and weighted distances (with positive weights). The proposed definition is applicable to general dimensions and covers in its gamut various regular curves and surfaces like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids, Cartesian k-ovals, etc. Several interesting properties are presented for this class of digital primitives such as space partitioning, topological separation, and connectivity properties. To demonstrate further the potential of this new way of defining digital primitives, we propose, as extension, another class of digital conics defined by focus-directrix combination. alternative_title: - LNCS article_processing_charge: No author: - first_name: Eric full_name: Andres, Eric last_name: Andres - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: 'Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal set. In: 20th IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:388-398. doi:10.1007/978-3-319-66272-5_31' apa: 'Andres, E., Biswas, R., & Bhowmick, P. (2017). Digital primitives defined by weighted focal set. In 20th IAPR International Conference (Vol. 10502, pp. 388–398). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_31' chicago: 'Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives Defined by Weighted Focal Set.” In 20th IAPR International Conference, 10502:388–98. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_31.' ieee: E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted focal set,” in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502, pp. 388–398. ista: 'Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted focal set. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.' mla: Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” 20th IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 388–98, doi:10.1007/978-3-319-66272-5_31. short: E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 388–398. conference: end_date: 2017-09-21 location: Vienna, Austria name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery' start_date: 2017-09-19 date_created: 2019-01-08T20:42:39Z date_published: 2017-08-22T00:00:00Z date_updated: 2022-01-27T15:38:35Z day: '22' doi: 10.1007/978-3-319-66272-5_31 extern: '1' intvolume: ' 10502' language: - iso: eng month: '08' oa_version: None page: 388-398 place: Cham publication: 20th IAPR International Conference publication_identifier: eisbn: - 978-3-319-66272-5 eissn: - 1611-3349 isbn: - 978-3-319-66271-8 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Digital primitives defined by weighted focal set type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 10502 year: '2017' ... --- _id: '593' abstract: - lang: eng text: Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements. author: - first_name: Nils full_name: Engelsen, Nils last_name: Engelsen - first_name: Rajiv full_name: Krishnakumar, Rajiv last_name: Krishnakumar - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Mark full_name: Kasevich, Mark last_name: Kasevich citation: ama: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 2017;118(14). doi:10.1103/PhysRevLett.118.140401 apa: Engelsen, N., Krishnakumar, R., Hosten, O., & Kasevich, M. (2017). Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.140401 chicago: Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.140401. ieee: N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations in spin-squeezed states of 500 000 atoms,” Physical Review Letters, vol. 118, no. 14. American Physical Society, 2017. ista: Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14). mla: Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters, vol. 118, no. 14, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.140401. short: N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:47:23Z date_published: 2017-04-03T00:00:00Z date_updated: 2021-01-12T08:05:16Z day: '03' doi: 10.1103/PhysRevLett.118.140401 extern: '1' intvolume: ' 118' issue: '14' language: - iso: eng month: '04' oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7212' status: public title: Bell correlations in spin-squeezed states of 500 000 atoms type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2017' ... --- _id: '600' abstract: - lang: eng text: Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase. article_processing_charge: No author: - first_name: Christoph full_name: Engel, Christoph last_name: Engel - first_name: Tobias full_name: Gubbey, Tobias last_name: Gubbey - first_name: Simon full_name: Neyer, Simon last_name: Neyer - first_name: Sarah full_name: Sainsbury, Sarah last_name: Sainsbury - first_name: Christiane full_name: Oberthuer, Christiane last_name: Oberthuer - first_name: Carlo full_name: Baejen, Carlo last_name: Baejen - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Patrick full_name: Cramer, Patrick last_name: Cramer citation: ama: Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription initiation. Cell. 2017;169(1):120-131.e22. doi:10.1016/j.cell.2017.03.003 apa: Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C., … Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.03.003 chicago: Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis of RNA Polymerase I Transcription Initiation.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.03.003. ieee: C. Engel et al., “Structural basis of RNA polymerase I transcription initiation,” Cell, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017. ista: Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation. Cell. 169(1), 120–131.e22. mla: Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription Initiation.” Cell, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:10.1016/j.cell.2017.03.003. short: C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C. Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22. date_created: 2018-12-11T11:47:25Z date_published: 2017-03-23T00:00:00Z date_updated: 2021-01-12T08:05:36Z day: '23' doi: 10.1016/j.cell.2017.03.003 extern: '1' intvolume: ' 169' issue: '1' language: - iso: eng month: '03' oa_version: None page: 120 - 131.e22 publication: Cell publication_identifier: issn: - '00928674' publication_status: published publisher: Cell Press publist_id: '7204' quality_controlled: '1' status: public title: Structural basis of RNA polymerase I transcription initiation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 169 year: '2017' ...