--- _id: '356' abstract: - lang: eng text: Cu2ZnSnS4, based on abundant and environmental friendly elements and with a direct band gap of 1.5 eV, is a main candidate material for solar energy conversion through both photovoltaics and photocatalysis. We detail here the synthesis of quasi-spherical Cu 2ZnSnS4 nanoparticles with unprecedented narrow size distributions. We further detail their use as seeds to produce CZTS-Au and CZTS-Pt heterostructured nanoparticles. Such heterostructured nanoparticles are shown to have excellent photocatalytic properties toward degradation of Rhodamine B and hydrogen generation by water splitting. acknowledgement: This work was supported by the European Regional Development Funds and the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486). article_processing_charge: No article_type: original author: - first_name: Xuelian full_name: Yu, Xuelian last_name: Yu - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Xiaoqiang full_name: An, Xiaoqiang last_name: An - first_name: Zhishan full_name: Luo, Zhishan last_name: Luo - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Yu X, Shavel A, An X, Luo Z, Ibáñez M, Cabot A. Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation. Journal of the American Chemical Society. 2014;136(26):9236-9239. doi:10.1021/ja502076b apa: Yu, X., Shavel, A., An, X., Luo, Z., Ibáñez, M., & Cabot, A. (2014). Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja502076b chicago: Yu, Xuelian, Alexey Shavel, Xiaoqiang An, Zhishan Luo, Maria Ibáñez, and Andreu Cabot. “Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au Heterostructured Nanoparticles for Photocatalytic Water Splitting and Pollutant Degradation.” Journal of the American Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja502076b. ieee: X. Yu, A. Shavel, X. An, Z. Luo, M. Ibáñez, and A. Cabot, “Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation,” Journal of the American Chemical Society, vol. 136, no. 26. American Chemical Society, pp. 9236–9239, 2014. ista: Yu X, Shavel A, An X, Luo Z, Ibáñez M, Cabot A. 2014. Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation. Journal of the American Chemical Society. 136(26), 9236–9239. mla: Yu, Xuelian, et al. “Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au Heterostructured Nanoparticles for Photocatalytic Water Splitting and Pollutant Degradation.” Journal of the American Chemical Society, vol. 136, no. 26, American Chemical Society, 2014, pp. 9236–39, doi:10.1021/ja502076b. short: X. Yu, A. Shavel, X. An, Z. Luo, M. Ibáñez, A. Cabot, Journal of the American Chemical Society 136 (2014) 9236–9239. date_created: 2018-12-11T11:46:00Z date_published: 2014-07-02T00:00:00Z date_updated: 2021-01-12T07:44:18Z day: '02' doi: 10.1021/ja502076b extern: '1' intvolume: ' 136' issue: '26' language: - iso: eng month: '07' oa_version: None page: 9236 - 9239 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7472' quality_controlled: '1' status: public title: Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2014' ... --- _id: '358' abstract: - lang: eng text: Monodispersed Pt3Sn nanoparticles were prepared through a mild thermal synthesis in the presence of surfactants. The performance of Pt3Sn for the electrooxidation of ethanol and adsorbed carbon monoxide (COad) in acid medium was studied by a combination of electrochemical and insitu spectroscopic methods, namely, infrared reflection absorption spectroscopy and differential electrochemical mass spectrometry (DEMS), and the results were compared to those obtained with the use of Pt black. The formation of the Pt3Sn solid solution promoted the oxidation of COad at less-positive potentials than those required for Pt black. Also, the electrooxidation of ethanol, especially at lower potentials, was more favorable with Pt3Sn, as deduced from the higher faradaic currents recorded during the ethanol oxidation reaction (EOR). However, the distribution of products as deduced by DEMS analysis suggested that the formation of C1 products, CO2 inclusive, is less significant on Pt3Sn than on Pt. In fact, the higher faradaic current recorded with the former catalyst can be attributed to the greater amounts of acetaldehyde and acetic acid formed. After the EOR, the surface of both Pt and Pt3Sn remained covered by ethanol adsorbates. Whereas C2 fragments were the main adsorbates at the surface of Pt3Sn after the EOR, both C1 and C2 species remained adsorbed at Pt black. acknowledgement: The Spanish Ministry of Science and Innovation (Project ENE2010–15381) and the CSIC (Project 201080E116) are acknowledged for financial support. article_processing_charge: No article_type: original author: - first_name: Tirma full_name: Herranz, Tirma last_name: Herranz - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: José full_name: Gómez De La Fuente, José last_name: Gómez De La Fuente - first_name: Francisco full_name: Pérez Alonso, Francisco last_name: Pérez Alonso - first_name: Miguel full_name: Peña, Miguel last_name: Peña - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Sergio full_name: Rojas, Sergio last_name: Rojas citation: ama: Herranz T, Ibáñez M, Gómez De La Fuente J, et al. In situ study of ethanol electrooxidation on monodispersed Pt inf 3 inf Sn nanoparticles. ChemElectroChem. 2014;1(5):885-895. doi:10.1002/celc.201300254 apa: Herranz, T., Ibáñez, M., Gómez De La Fuente, J., Pérez Alonso, F., Peña, M., Cabot, A., & Rojas, S. (2014). In situ study of ethanol electrooxidation on monodispersed Pt inf 3 inf Sn nanoparticles. ChemElectroChem. Wiley-Blackwell. https://doi.org/10.1002/celc.201300254 chicago: Herranz, Tirma, Maria Ibáñez, José Gómez De La Fuente, Francisco Pérez Alonso, Miguel Peña, Andreu Cabot, and Sergio Rojas. “In Situ Study of Ethanol Electrooxidation on Monodispersed Pt Inf 3 Inf Sn Nanoparticles.” ChemElectroChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/celc.201300254. ieee: T. Herranz et al., “In situ study of ethanol electrooxidation on monodispersed Pt inf 3 inf Sn nanoparticles,” ChemElectroChem, vol. 1, no. 5. Wiley-Blackwell, pp. 885–895, 2014. ista: Herranz T, Ibáñez M, Gómez De La Fuente J, Pérez Alonso F, Peña M, Cabot A, Rojas S. 2014. In situ study of ethanol electrooxidation on monodispersed Pt inf 3 inf Sn nanoparticles. ChemElectroChem. 1(5), 885–895. mla: Herranz, Tirma, et al. “In Situ Study of Ethanol Electrooxidation on Monodispersed Pt Inf 3 Inf Sn Nanoparticles.” ChemElectroChem, vol. 1, no. 5, Wiley-Blackwell, 2014, pp. 885–95, doi:10.1002/celc.201300254. short: T. Herranz, M. Ibáñez, J. Gómez De La Fuente, F. Pérez Alonso, M. Peña, A. Cabot, S. Rojas, ChemElectroChem 1 (2014) 885–895. date_created: 2018-12-11T11:46:00Z date_published: 2014-03-03T00:00:00Z date_updated: 2021-01-12T07:44:26Z day: '03' doi: 10.1002/celc.201300254 extern: '1' intvolume: ' 1' issue: '5' language: - iso: eng month: '03' oa_version: None page: 885 - 895 publication: ChemElectroChem publication_status: published publisher: Wiley-Blackwell publist_id: '7474' quality_controlled: '1' status: public title: In situ study of ethanol electrooxidation on monodispersed Pt inf 3 inf Sn nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2014' ... --- _id: '451' abstract: - lang: eng text: We introduce algorithms for the computation of homology, cohomology, and related operations on cubical cell complexes, using the technique based on a chain contraction from the original chain complex to a reduced one that represents its homology. This work is based on previous results for simplicial complexes, and uses Serre’s diagonalization for cubical cells. An implementation in C++ of the introduced algorithms is available at http://www.pawelpilarczyk.com/chaincon/ together with some examples. The paper is self-contained as much as possible, and is written at a very elementary level, so that basic knowledge of algebraic topology should be sufficient to follow it. acknowledgement: 'This research was partially supported from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Compe titividade (POFC) and from the Portuguese national funds through Fundacaoparaa Ciencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645(ref. FCT PTDC/MAT/098871/2008), as well as from the funds distributed through the European Science Foundation (ESF) Research Networking Programme on “Applied and Computational Algebraic Topology” (ACAT). P.Real was additionally supported by the Spanish Ministry of Science and Innovation, project no. MTM2009-12716. ' author: - first_name: Pawel full_name: Pawel Pilarczyk id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk - first_name: Pedro full_name: Real, Pedro last_name: Real citation: ama: Pilarczyk P, Real P. Computation of cubical homology, cohomology, and (co)homological operations via chain contraction. Advances in Computational Mathematics. 2014;41(1):253-275. doi:10.1007/s10444-014-9356-1 apa: Pilarczyk, P., & Real, P. (2014). Computation of cubical homology, cohomology, and (co)homological operations via chain contraction. Advances in Computational Mathematics. Kluwer. https://doi.org/10.1007/s10444-014-9356-1 chicago: Pilarczyk, Pawel, and Pedro Real. “Computation of Cubical Homology, Cohomology, and (Co)Homological Operations via Chain Contraction.” Advances in Computational Mathematics. Kluwer, 2014. https://doi.org/10.1007/s10444-014-9356-1. ieee: P. Pilarczyk and P. Real, “Computation of cubical homology, cohomology, and (co)homological operations via chain contraction,” Advances in Computational Mathematics, vol. 41, no. 1. Kluwer, pp. 253–275, 2014. ista: Pilarczyk P, Real P. 2014. Computation of cubical homology, cohomology, and (co)homological operations via chain contraction. Advances in Computational Mathematics. 41(1), 253–275. mla: Pilarczyk, Pawel, and Pedro Real. “Computation of Cubical Homology, Cohomology, and (Co)Homological Operations via Chain Contraction.” Advances in Computational Mathematics, vol. 41, no. 1, Kluwer, 2014, pp. 253–75, doi:10.1007/s10444-014-9356-1. short: P. Pilarczyk, P. Real, Advances in Computational Mathematics 41 (2014) 253–275. date_created: 2018-12-11T11:46:33Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T07:59:20Z day: '01' doi: 10.1007/s10444-014-9356-1 extern: 1 intvolume: ' 41' issue: '1' main_file_link: - open_access: '1' url: https://idus.us.es/xmlui/handle/11441/38719 month: '01' oa: 1 page: 253 - 275 publication: Advances in Computational Mathematics publication_status: published publisher: Kluwer publist_id: '7371' quality_controlled: 0 status: public title: Computation of cubical homology, cohomology, and (co)homological operations via chain contraction type: journal_article volume: 41 year: '2014' ... --- _id: '468' abstract: - lang: eng text: Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance) is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss. acknowledgement: The study was funded by the University of Vienna (Focus of Excellence grant), the Galápagos Conservation Trust, and the Ethologische Gesellschaft e.V. article_number: '0107518' author: - first_name: Arno full_name: Cimadom, Arno last_name: Cimadom - first_name: Angel full_name: Ulloa, Angel last_name: Ulloa - first_name: Patrick full_name: Meidl, Patrick id: 4709BCE6-F248-11E8-B48F-1D18A9856A87 last_name: Meidl - first_name: Markus full_name: Zöttl, Markus last_name: Zöttl - first_name: Elisabet full_name: Zöttl, Elisabet last_name: Zöttl - first_name: Birgit full_name: Fessl, Birgit last_name: Fessl - first_name: Erwin full_name: Nemeth, Erwin last_name: Nemeth - first_name: Michael full_name: Dvorak, Michael last_name: Dvorak - first_name: Francesca full_name: Cunninghame, Francesca last_name: Cunninghame - first_name: Sabine full_name: Tebbich, Sabine last_name: Tebbich citation: ama: Cimadom A, Ulloa A, Meidl P, et al. Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107518 apa: Cimadom, A., Ulloa, A., Meidl, P., Zöttl, M., Zöttl, E., Fessl, B., … Tebbich, S. (2014). Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107518 chicago: Cimadom, Arno, Angel Ulloa, Patrick Meidl, Markus Zöttl, Elisabet Zöttl, Birgit Fessl, Erwin Nemeth, Michael Dvorak, Francesca Cunninghame, and Sabine Tebbich. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding Success in Darwin’s Finches.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107518. ieee: A. Cimadom et al., “Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014. ista: Cimadom A, Ulloa A, Meidl P, Zöttl M, Zöttl E, Fessl B, Nemeth E, Dvorak M, Cunninghame F, Tebbich S. 2014. Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin’s finches. PLoS One. 9(9), 0107518. mla: Cimadom, Arno, et al. “Invasive Parasites Habitat Change and Heavy Rainfall Reduce Breeding Success in Darwin’s Finches.” PLoS One, vol. 9, no. 9, 0107518, Public Library of Science, 2014, doi:10.1371/journal.pone.0107518. short: A. Cimadom, A. Ulloa, P. Meidl, M. Zöttl, E. Zöttl, B. Fessl, E. Nemeth, M. Dvorak, F. Cunninghame, S. Tebbich, PLoS One 9 (2014). date_created: 2018-12-11T11:46:38Z date_published: 2014-09-23T00:00:00Z date_updated: 2021-01-12T08:00:48Z day: '23' ddc: - '576' department: - _id: CampIT doi: 10.1371/journal.pone.0107518 file: - access_level: open_access checksum: b24e7518ccd41effed0d7d9e2498f67f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:48Z date_updated: 2020-07-14T12:46:34Z file_id: '5103' file_name: IST-2018-954-v1+1_2014_Meidl_Invasive_parasites.PDF file_size: 489387 relation: main_file file_date_updated: 2020-07-14T12:46:34Z has_accepted_license: '1' intvolume: ' 9' issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '09' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '7352' pubrep_id: '954' quality_controlled: '1' scopus_import: 1 status: public title: Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin's finches 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '475' abstract: - lang: eng text: 'First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard. ' alternative_title: - EPTCS author: - first_name: Benjamin full_name: Aminof, Benjamin id: 4A55BD00-F248-11E8-B48F-1D18A9856A87 last_name: Aminof - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin citation: ama: 'Aminof B, Rubin S. First cycle games. In: Electronic Proceedings in Theoretical Computer Science, EPTCS. Vol 146. Open Publishing Association; 2014:83-90. doi:10.4204/EPTCS.146.11' apa: 'Aminof, B., & Rubin, S. (2014). First cycle games. In Electronic Proceedings in Theoretical Computer Science, EPTCS (Vol. 146, pp. 83–90). Grenoble, France: Open Publishing Association. https://doi.org/10.4204/EPTCS.146.11' chicago: Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” In Electronic Proceedings in Theoretical Computer Science, EPTCS, 146:83–90. Open Publishing Association, 2014. https://doi.org/10.4204/EPTCS.146.11. ieee: B. Aminof and S. Rubin, “First cycle games,” in Electronic Proceedings in Theoretical Computer Science, EPTCS, Grenoble, France, 2014, vol. 146, pp. 83–90. ista: 'Aminof B, Rubin S. 2014. First cycle games. Electronic Proceedings in Theoretical Computer Science, EPTCS. SR: Strategic Reasoning, EPTCS, vol. 146, 83–90.' mla: Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” Electronic Proceedings in Theoretical Computer Science, EPTCS, vol. 146, Open Publishing Association, 2014, pp. 83–90, doi:10.4204/EPTCS.146.11. short: B. Aminof, S. Rubin, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing Association, 2014, pp. 83–90. conference: end_date: 2014-04-06 location: Grenoble, France name: 'SR: Strategic Reasoning' start_date: 2014-04-05 date_created: 2018-12-11T11:46:41Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T08:00:53Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4204/EPTCS.146.11 ec_funded: 1 file: - access_level: open_access checksum: 4d7b4ab82980cca2b96ac7703992a8c8 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:08Z date_updated: 2020-07-14T12:46:35Z file_id: '5260' file_name: IST-2018-952-v1+1_2014_Rubin_First_cycle.pdf file_size: 100115 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 146' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 83 - 90 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _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' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Electronic Proceedings in Theoretical Computer Science, EPTCS publication_status: published publisher: Open Publishing Association publist_id: '7345' pubrep_id: '952' quality_controlled: '1' scopus_import: 1 status: public title: First cycle 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2014' ... --- _id: '10892' abstract: - lang: eng text: "In this paper, 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.\r\nUsing 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: 'T. Biedl was supported by NSERC and the Ross and Muriel Cheriton Fellowship. P. Palfrader was supported by Austrian Science Fund (FWF): P25816-N15.' alternative_title: - LNCS article_processing_charge: No 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. In: 25th International Symposium, ISAAC 2014. Vol 8889. Springer Nature; 2014:117-127. doi:10.1007/978-3-319-13075-0_10' apa: 'Biedl, T., Huber, S., & Palfrader, P. (2014). Planar matchings for weighted straight skeletons. In 25th International Symposium, ISAAC 2014 (Vol. 8889, pp. 117–127). Jeonju, Korea: Springer Nature. https://doi.org/10.1007/978-3-319-13075-0_10' chicago: Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” In 25th International Symposium, ISAAC 2014, 8889:117–27. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13075-0_10. ieee: T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” in 25th International Symposium, ISAAC 2014, Jeonju, Korea, 2014, vol. 8889, pp. 117–127. ista: 'Biedl T, Huber S, Palfrader P. 2014. Planar matchings for weighted straight skeletons. 25th International Symposium, ISAAC 2014. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 8889, 117–127.' mla: Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” 25th International Symposium, ISAAC 2014, vol. 8889, Springer Nature, 2014, pp. 117–27, doi:10.1007/978-3-319-13075-0_10. short: T. Biedl, S. Huber, P. Palfrader, in:, 25th International Symposium, ISAAC 2014, Springer Nature, 2014, pp. 117–127. conference: end_date: 2014-12-17 location: Jeonju, Korea name: 'ISAAC: International Symposium on Algorithms and Computation' start_date: 2014-12-15 date_created: 2022-03-21T07:09:03Z date_published: 2014-11-08T00:00:00Z date_updated: 2023-02-23T12:20:55Z day: '08' department: - _id: HeEd doi: 10.1007/978-3-319-13075-0_10 intvolume: ' 8889' language: - iso: eng month: '11' oa_version: None page: 117-127 publication: 25th International Symposium, ISAAC 2014 publication_identifier: eisbn: - '9783319130750' eissn: - 1611-3349 isbn: - '9783319130743' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '481' relation: later_version status: public scopus_import: '1' status: public title: Planar matchings for weighted straight skeletons type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8889 year: '2014' ... --- _id: '537' abstract: - lang: eng text: Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring. author: - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Thomas full_name: Ezard, Thomas last_name: Ezard - first_name: Rebecca full_name: Hoyle, Rebecca last_name: Hoyle citation: ama: Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150 apa: Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150 chicago: Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1150. ieee: R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014. ista: Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145. mla: Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:10.1002/ece3.1150. short: R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145. date_created: 2018-12-11T11:47:02Z date_published: 2014-07-19T00:00:00Z date_updated: 2021-01-12T08:01:30Z day: '19' ddc: - '530' - '571' department: - _id: NiBa - _id: GaTk doi: 10.1002/ece3.1150 file: - access_level: open_access checksum: e32abf75a248e7a11811fd7f60858769 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:31Z date_updated: 2020-07-14T12:46:38Z file_id: '4886' file_name: IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf file_size: 621582 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 4' issue: '15' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 3139 - 3145 publication: Ecology and Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '7280' pubrep_id: '934' scopus_import: 1 status: public title: Fitness consequences of maternal and grandmaternal effects 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: 4 year: '2014' ... --- _id: '1903' abstract: - lang: eng text: 'We consider two-player zero-sum partial-observation stochastic games on graphs. Based on the information available to the players these games can be classified as follows: (a) general partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) perfect-observation (both players have complete view of the game). The one-sided partial-observation games subsumes the important special case of one-player partial-observation stochastic games (or partial-observation Markov decision processes (POMDPs)). Based on the randomization available for the strategies, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. We consider all these classes of games with reachability, and parity objectives that can express all ω-regular objectives. The analysis problems are classified into the qualitative analysis that asks for the existence of a strategy that ensures the objective with probability 1; and the quantitative analysis that asks for the existence of a strategy that ensures the objective with probability at least λ (0,1). In this talk we will cover a wide range of results: for perfect-observation games; for POMDPs; for one-sided partial-observation games; and for general partial-observation games.' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Partial-observation stochastic reachability and parity games. In: Vol 8634. Springer; 2014:1-4. doi:10.1007/978-3-662-44522-8_1' apa: 'Chatterjee, K. (2014). Partial-observation stochastic reachability and parity games (Vol. 8634, pp. 1–4). Presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary: Springer. https://doi.org/10.1007/978-3-662-44522-8_1' chicago: Chatterjee, Krishnendu. “Partial-Observation Stochastic Reachability and Parity Games,” 8634:1–4. Springer, 2014. https://doi.org/10.1007/978-3-662-44522-8_1. ieee: 'K. Chatterjee, “Partial-observation stochastic reachability and parity games,” presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary, 2014, vol. 8634, no. PART 1, pp. 1–4.' ista: 'Chatterjee K. 2014. Partial-observation stochastic reachability and parity games. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 8634, 1–4.' mla: Chatterjee, Krishnendu. Partial-Observation Stochastic Reachability and Parity Games. Vol. 8634, no. PART 1, Springer, 2014, pp. 1–4, doi:10.1007/978-3-662-44522-8_1. short: K. Chatterjee, in:, Springer, 2014, pp. 1–4. conference: end_date: 2014-08-29 location: Budapest, Hungary name: 'MFCS: Mathematical Foundations of Computer Science' start_date: 2014-08-25 date_created: 2018-12-11T11:54:38Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T12:23:43Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-44522-8_1 ec_funded: 1 intvolume: ' 8634' issue: PART 1 language: - iso: eng month: '01' oa_version: None page: 1 - 4 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' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '5192' pubrep_id: '141' quality_controlled: '1' related_material: record: - id: '2211' relation: later_version status: public - id: '5381' relation: earlier_version status: public scopus_import: 1 status: public title: Partial-observation stochastic reachability and parity games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8634 year: '2014' ... --- _id: '2211' abstract: - lang: eng text: 'In two-player finite-state stochastic games of partial observation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distribution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or positively (i.e., with positive probability), no matter the strategy of the second player. We classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two-sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Our main results for pure strategies are as follows: (1) For one-sided games with player 2 having perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strategies are not sufficient, and we present an exponential upper bound on memory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algorithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 having perfect observation we show that nonelementarymemory is both necessary and sufficient for both almost-sure and positive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least nonelementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence result exhibit serious flaws in previous results of the literature: we show a nonelementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed.' article_number: '16' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic (TOCL). 2014;15(2). doi:10.1145/2579821' apa: 'Chatterjee, K., & Doyen, L. (2014). Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2579821' chicago: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic (TOCL). ACM, 2014. https://doi.org/10.1145/2579821.' ieee: 'K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to win when belief fails,” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 2. ACM, 2014.' ista: 'Chatterjee K, Doyen L. 2014. Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic (TOCL). 15(2), 16.' mla: 'Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 2, 16, ACM, 2014, doi:10.1145/2579821.' short: K. Chatterjee, L. Doyen, ACM Transactions on Computational Logic (TOCL) 15 (2014). date_created: 2018-12-11T11:56:21Z date_published: 2014-04-01T00:00:00Z date_updated: 2023-02-23T12:23:43Z day: '01' department: - _id: KrCh doi: 10.1145/2579821 external_id: arxiv: - '1107.2141' intvolume: ' 15' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1107.2141 month: '04' oa: 1 oa_version: Preprint publication: ACM Transactions on Computational Logic (TOCL) publication_status: published publisher: ACM publist_id: '4759' quality_controlled: '1' related_material: record: - id: '1903' relation: earlier_version status: public - id: '2955' relation: earlier_version status: public - id: '5381' relation: earlier_version status: public scopus_import: 1 status: public title: 'Partial-observation stochastic games: How to win when belief fails' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '2038' abstract: - lang: eng text: Recently, there has been an effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions. At the heart of quantitative objectives lies the accumulation of values along a computation. It is often the accumulated sum, as with energy objectives, or the accumulated average, as with mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point in time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire infinite computation. We study the border of decidability for such quantitative extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with both prefix-accumulation assertions, or extending LTL with both path-accumulation assertions, results in temporal logics whose model-checking problem is decidable. Moreover, the prefix-accumulation assertions may be generalized with "controlled accumulation," allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that this branching-time logic is, in a sense, the maximal logic with one or both of the prefix-accumulation assertions that permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL, makes the problem undecidable. acknowledgement: The research was supported in part by ERC Starting grant 278410 (QUALITY). article_number: '27' article_processing_charge: No article_type: original author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - 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: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 2014;15(4). doi:10.1145/2629686 apa: Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2014). Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2629686 chicago: Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic (TOCL). ACM, 2014. https://doi.org/10.1145/2629686. ieee: U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications with accumulative values,” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 4. ACM, 2014. ista: Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 15(4), 27. mla: Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 4, 27, ACM, 2014, doi:10.1145/2629686. short: U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 15 (2014). date_created: 2018-12-11T11:55:21Z date_published: 2014-09-16T00:00:00Z date_updated: 2023-02-23T12:23:54Z day: '16' ddc: - '000' - '004' department: - _id: ToHe - _id: KrCh doi: 10.1145/2629686 ec_funded: 1 file: - access_level: open_access checksum: 354c41d37500b56320afce94cf9a99c2 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:59Z date_updated: 2020-07-14T12:45:26Z file_id: '4851' file_name: IST-2014-192-v1+1_AccumulativeValues.pdf file_size: 346184 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 15' issue: '4' language: - iso: eng month: '09' oa: 1 oa_version: Submitted 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: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _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' - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ACM Transactions on Computational Logic (TOCL) publication_status: published publisher: ACM publist_id: '5013' pubrep_id: '192' quality_controlled: '1' related_material: record: - id: '3356' relation: earlier_version status: public - id: '5385' relation: earlier_version status: public scopus_import: 1 status: public title: Temporal specifications with accumulative values type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '2162' abstract: - lang: eng text: 'We study two-player (zero-sum) concurrent mean-payoff games played on a finite-state graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lies in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP ∩ coNP is the long-standing best known bound). We present a variant of the strategy-iteration algorithm by Hoffman and Karp; show that both our algorithm and the classical value-iteration algorithm can approximate the value in exponential time; and identify a subclass where the value-iteration algorithm is a FPTAS. We also show that the exact value can be expressed in the existential theory of the reals, and establish square-root sum hardness for a related class of games.' alternative_title: - LNCS 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 citation: ama: 'Chatterjee K, Ibsen-Jensen R. The complexity of ergodic mean payoff games. In: Vol 8573. Springer; 2014:122-133. doi:10.1007/978-3-662-43951-7_11' apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2014). The complexity of ergodic mean payoff games (Vol. 8573, pp. 122–133). Presented at the ICST: International Conference on Software Testing, Verification and Validation, Copenhagen, Denmark: Springer. https://doi.org/10.1007/978-3-662-43951-7_11' chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Ergodic Mean Payoff Games,” 8573:122–33. Springer, 2014. https://doi.org/10.1007/978-3-662-43951-7_11. ieee: 'K. Chatterjee and R. Ibsen-Jensen, “The complexity of ergodic mean payoff games,” presented at the ICST: International Conference on Software Testing, Verification and Validation, Copenhagen, Denmark, 2014, vol. 8573, no. Part 2, pp. 122–133.' ista: 'Chatterjee K, Ibsen-Jensen R. 2014. The complexity of ergodic mean payoff games. ICST: International Conference on Software Testing, Verification and Validation, LNCS, vol. 8573, 122–133.' mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic Mean Payoff Games. Vol. 8573, no. Part 2, Springer, 2014, pp. 122–33, doi:10.1007/978-3-662-43951-7_11. short: K. Chatterjee, R. Ibsen-Jensen, in:, Springer, 2014, pp. 122–133. conference: end_date: 2014-07-11 location: Copenhagen, Denmark name: 'ICST: International Conference on Software Testing, Verification and Validation' start_date: 2014-07-08 date_created: 2018-12-11T11:56:04Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T12:24:48Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-43951-7_11 ec_funded: 1 external_id: arxiv: - '1404.5734' intvolume: ' 8573' issue: Part 2 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.5734 month: '01' oa: 1 oa_version: Preprint page: 122 - 133 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' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4822' quality_controlled: '1' related_material: record: - id: '5404' relation: earlier_version status: public status: public title: The complexity of ergodic mean payoff games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8573 year: '2014' ... --- _id: '2213' abstract: - lang: eng text: We consider two-player partial-observation stochastic games on finitestate graphs where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are ε-regular conditions specified as parity objectives. The qualitative-analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). These qualitative-analysis problems are known to be undecidable. However in many applications the relevant question is the existence of finite-memory strategies, and the qualitative-analysis problems under finite-memory strategies was recently shown to be decidable in 2EXPTIME.We improve the complexity and show that the qualitative-analysis problems for partial-observation stochastic parity games under finite-memory strategies are EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis. acknowledgement: 'This research was supported by European project Cassting (FP7-601148), NSF grants CNS 1049862 and CCF-1139011, by NSF Expe ditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Sumit full_name: Nain, Sumit last_name: Nain - first_name: Moshe full_name: Vardi, Moshe last_name: Vardi citation: ama: 'Chatterjee K, Doyen L, Nain S, Vardi M. The complexity of partial-observation stochastic parity games with finite-memory strategies. In: Vol 8412. Springer; 2014:242-257. doi:10.1007/978-3-642-54830-7_16' apa: 'Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2014). The complexity of partial-observation stochastic parity games with finite-memory strategies (Vol. 8412, pp. 242–257). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_16' chicago: Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. “The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies,” 8412:242–57. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_16. ieee: 'K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, “The complexity of partial-observation stochastic parity games with finite-memory strategies,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 242–257.' ista: 'Chatterjee K, Doyen L, Nain S, Vardi M. 2014. The complexity of partial-observation stochastic parity games with finite-memory strategies. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 242–257.' mla: Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. Vol. 8412, Springer, 2014, pp. 242–57, doi:10.1007/978-3-642-54830-7_16. short: K. Chatterjee, L. Doyen, S. Nain, M. Vardi, in:, Springer, 2014, pp. 242–257. conference: end_date: 2014-04-13 location: Grenoble, France name: 'FoSSaCS: Foundations of Software Science and Computation Structures' start_date: 2014-04-05 date_created: 2018-12-11T11:56:21Z date_published: 2014-04-01T00:00:00Z date_updated: 2023-02-23T12:24:58Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-54830-7_16 ec_funded: 1 external_id: arxiv: - '1401.3289' intvolume: ' 8412' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1401.3289 month: '04' oa: 1 oa_version: Preprint page: 242 - 257 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' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4757' quality_controlled: '1' related_material: record: - id: '5408' relation: earlier_version status: public scopus_import: 1 status: public title: The complexity of partial-observation stochastic parity games with finite-memory strategies type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8412 year: '2014' ... --- _id: '2212' abstract: - lang: eng text: 'The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2 1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic). We present an algorithm running in time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which the objective can be ensured with probability 1, where n is the number of states of the game, d the number of priorities of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states in 2 1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective). ' acknowledgement: "This research was supported by European project Cassting (FP7-601148).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/128." alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Hugo full_name: Gimbert, Hugo last_name: Gimbert - first_name: Youssouf full_name: Oualhadj, Youssouf last_name: Oualhadj citation: ama: 'Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-information stochastic mean-payoff parity games. In: Vol 8412. Springer; 2014:210-225. doi:10.1007/978-3-642-54830-7_14' apa: 'Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2014). Perfect-information stochastic mean-payoff parity games (Vol. 8412, pp. 210–225). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_14' chicago: Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. “Perfect-Information Stochastic Mean-Payoff Parity Games,” 8412:210–25. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_14. ieee: 'K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, “Perfect-information stochastic mean-payoff parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 210–225.' ista: 'Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2014. Perfect-information stochastic mean-payoff parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 210–225.' mla: Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff Parity Games. Vol. 8412, Springer, 2014, pp. 210–25, doi:10.1007/978-3-642-54830-7_14. short: K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, in:, Springer, 2014, pp. 210–225. conference: end_date: 2014-04-13 location: Grenoble, France name: 'FoSSaCS: Foundations of Software Science and Computation Structures' start_date: 2014-04-05 date_created: 2018-12-11T11:56:21Z date_published: 2014-04-01T00:00:00Z date_updated: 2023-02-23T12:24:50Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-54830-7_14 ec_funded: 1 intvolume: ' 8412' language: - iso: eng month: '04' oa_version: None page: 210 - 225 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' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4758' quality_controlled: '1' related_material: record: - id: '5405' relation: earlier_version status: public scopus_import: 1 status: public title: Perfect-information stochastic mean-payoff parity games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8412 year: '2014' ... --- _id: '2216' abstract: - lang: eng text: The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in time stamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than δ away from the parameter, for δ > 0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and analogous decidability results hold for rectangular automata. 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: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: 'Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit distance for timed automata. In: Springer; 2014:303-312. doi:10.1145/2562059.2562141' apa: 'Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2014). Edit distance for timed automata (pp. 303–312). Presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562141' chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Ritankar Majumdar. “Edit Distance for Timed Automata,” 303–12. Springer, 2014. https://doi.org/10.1145/2562059.2562141. ieee: 'K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, “Edit distance for timed automata,” presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany, 2014, pp. 303–312.' ista: 'Chatterjee K, Ibsen-Jensen R, Majumdar R. 2014. Edit distance for timed automata. HSCC: Hybrid Systems - Computation and Control, 303–312.' mla: Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. Springer, 2014, pp. 303–12, doi:10.1145/2562059.2562141. short: K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, in:, Springer, 2014, pp. 303–312. conference: end_date: 2017-04-17 location: Berlin, Germany name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2017-04-15 date_created: 2018-12-11T11:56:22Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T12:25:01Z day: '01' department: - _id: KrCh doi: 10.1145/2562059.2562141 language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/citation.cfm?doid=2562059.2562141 month: '01' oa: 1 oa_version: Submitted Version page: 303 - 312 publication_status: published publisher: Springer publist_id: '4752' quality_controlled: '1' related_material: record: - id: '5409' relation: earlier_version status: public status: public title: Edit distance for timed automata type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5411' abstract: - lang: eng text: "Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing.\r\nIn this paper, we study compositional properties of the IOCO-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the IOCO conformance relation, the resulting methodology can be applied to a broader class of systems." alternative_title: - IST Austria Technical Report 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: Willibald full_name: Krenn, Willibald last_name: Krenn - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic citation: ama: Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional Specifications for IOCO Testing. IST Austria; 2014. doi:10.15479/AT:IST-2014-148-v2-1 apa: Daca, P., Henzinger, T. A., Krenn, W., & Nickovic, D. (2014). Compositional specifications for IOCO testing. IST Austria. https://doi.org/10.15479/AT:IST-2014-148-v2-1 chicago: Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. Compositional Specifications for IOCO Testing. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-148-v2-1. ieee: P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, Compositional specifications for IOCO testing. IST Austria, 2014. ista: Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing, IST Austria, 20p. mla: Daca, Przemyslaw, et al. Compositional Specifications for IOCO Testing. IST Austria, 2014, doi:10.15479/AT:IST-2014-148-v2-1. short: P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, Compositional Specifications for IOCO Testing, IST Austria, 2014. date_created: 2018-12-12T11:39:11Z date_published: 2014-01-28T00:00:00Z date_updated: 2023-02-23T10:31:07Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.15479/AT:IST-2014-148-v2-1 file: - access_level: open_access checksum: 0e03aba625cc334141a3148432aa5760 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:21Z date_updated: 2020-07-14T12:46:46Z file_id: '5543' file_name: IST-2014-148-v2+1_main_tr.pdf file_size: 534732 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '20' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '152' related_material: record: - id: '2167' relation: later_version status: public status: public title: Compositional specifications for IOCO testing type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5413' abstract: - lang: eng text: "We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.\r\nWe introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.\r\nWe present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik citation: ama: Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v2-2 apa: Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v2-2 chicago: Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v2-2. ieee: K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis of probabilistic systems. IST Austria, 2014. ista: Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic systems, IST Austria, 33p. mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v2-2. short: K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic Systems, IST Austria, 2014. date_created: 2018-12-12T11:39:11Z date_published: 2014-02-06T00:00:00Z date_updated: 2023-02-23T12:25:18Z day: '06' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2014-153-v2-2 file: - access_level: open_access checksum: ce4967a184d84863eec76c66cbac1614 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:17Z date_updated: 2020-07-14T12:46:47Z file_id: '5539' file_name: IST-2014-153-v2+2_main.pdf file_size: 606049 relation: main_file file_date_updated: 2020-07-14T12:46:47Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '33' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '164' related_material: record: - id: '2063' relation: later_version status: public - id: '5412' relation: earlier_version status: public - id: '5414' relation: later_version status: public status: public title: CEGAR for qualitative analysis of probabilistic systems type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5414' abstract: - lang: eng text: "We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.\r\nWe introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.\r\nWe present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. \r\nWe have implemented our algorithms and show that the compositional analysis leads to significant improvements. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik citation: ama: Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v3-1 apa: Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v3-1 chicago: Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v3-1. ieee: K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis of probabilistic systems. IST Austria, 2014. ista: Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic systems, IST Austria, 33p. mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v3-1. short: K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic Systems, IST Austria, 2014. date_created: 2018-12-12T11:39:12Z date_published: 2014-02-07T00:00:00Z date_updated: 2023-02-23T12:25:15Z day: '07' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2014-153-v3-1 file: - access_level: open_access checksum: 87b93fe9af71fc5c94b0eb6151537e11 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:03Z date_updated: 2020-07-14T12:46:48Z file_id: '5464' file_name: IST-2014-153-v3+1_main.pdf file_size: 606227 relation: main_file file_date_updated: 2020-07-14T12:46:48Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '33' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '165' related_material: record: - id: '2063' relation: later_version status: public - id: '5412' relation: earlier_version status: public - id: '5413' relation: earlier_version status: public status: public title: CEGAR for qualitative analysis of probabilistic systems type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5412' abstract: - lang: eng text: "We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.\r\nWe introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.\r\nWe present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik citation: ama: Chatterjee K, Daca P, Chmelik M. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-153-v1-1 apa: Chatterjee, K., Daca, P., & Chmelik, M. (2014). CEGAR for qualitative analysis of probabilistic systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-153-v1-1 chicago: Chatterjee, Krishnendu, Przemyslaw Daca, and Martin Chmelik. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-153-v1-1. ieee: K. Chatterjee, P. Daca, and M. Chmelik, CEGAR for qualitative analysis of probabilistic systems. IST Austria, 2014. ista: Chatterjee K, Daca P, Chmelik M. 2014. CEGAR for qualitative analysis of probabilistic systems, IST Austria, 31p. mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-153-v1-1. short: K. Chatterjee, P. Daca, M. Chmelik, CEGAR for Qualitative Analysis of Probabilistic Systems, IST Austria, 2014. date_created: 2018-12-12T11:39:11Z date_published: 2014-01-29T00:00:00Z date_updated: 2023-02-23T12:25:18Z day: '29' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2014-153-v1-1 file: - access_level: open_access checksum: 4d6cda4bebed970926403ad6ad8c745f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:39Z date_updated: 2020-07-14T12:46:47Z file_id: '5500' file_name: IST-2014-153-v1+1_main.pdf file_size: 423322 relation: main_file file_date_updated: 2020-07-14T12:46:47Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '31' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '153' related_material: record: - id: '2063' relation: later_version status: public - id: '5413' relation: later_version status: public - id: '5414' relation: later_version status: public status: public title: CEGAR for qualitative analysis of probabilistic systems type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2163' abstract: - lang: eng text: We consider multi-player graph games with partial-observation and parity objective. While the decision problem for three-player games with a coalition of the first and second players against the third player is undecidable in general, we present a decidability result for partial-observation games where the first and third player are in a coalition against the second player, thus where the second player is adversarial but weaker due to partial-observation. We establish tight complexity bounds in the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness for parity objectives. The symmetric case of player 1 more informed than player 2 is much more complicated, and we show that already in the case where player 1 has perfect observation, memory of size non-elementary is necessary in general for reachability objectives, and the problem is decidable for safety and reachability objectives. From our results we derive new complexity results for partial-observation stochastic games. acknowledgement: "This research was partly supported by European project Cassting (FP7-601148).\r\nTechnical Report under https://research-explorer.app.ist.ac.at/record/5418\r\n" alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: 'Chatterjee K, Doyen L. Games with a weak adversary. In: Lecture Notes in Computer Science. Vol 8573. Springer; 2014:110-121. doi:10.1007/978-3-662-43951-7_10' apa: 'Chatterjee, K., & Doyen, L. (2014). Games with a weak adversary. In Lecture Notes in Computer Science (Vol. 8573, pp. 110–121). Copenhagen, Denmark: Springer. https://doi.org/10.1007/978-3-662-43951-7_10' chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Games with a Weak Adversary.” In Lecture Notes in Computer Science, 8573:110–21. Springer, 2014. https://doi.org/10.1007/978-3-662-43951-7_10. ieee: K. Chatterjee and L. Doyen, “Games with a weak adversary,” in Lecture Notes in Computer Science, Copenhagen, Denmark, 2014, vol. 8573, no. Part 2, pp. 110–121. ista: 'Chatterjee K, Doyen L. 2014. Games with a weak adversary. Lecture Notes in Computer Science. ICALP: Automata, Languages and Programming, LNCS, vol. 8573, 110–121.' mla: Chatterjee, Krishnendu, and Laurent Doyen. “Games with a Weak Adversary.” Lecture Notes in Computer Science, vol. 8573, no. Part 2, Springer, 2014, pp. 110–21, doi:10.1007/978-3-662-43951-7_10. short: K. Chatterjee, L. Doyen, in:, Lecture Notes in Computer Science, Springer, 2014, pp. 110–121. conference: end_date: 2014-07-11 location: Copenhagen, Denmark name: 'ICALP: Automata, Languages and Programming' start_date: 2014-07-08 date_created: 2018-12-11T11:56:04Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T12:25:29Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-43951-7_10 ec_funded: 1 external_id: arxiv: - '1404.5453' intvolume: ' 8573' issue: Part 2 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1404.5453 month: '01' oa: 1 oa_version: Preprint page: 110 - 121 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' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Lecture Notes in Computer Science publication_status: published publisher: Springer publist_id: '4821' quality_controlled: '1' related_material: record: - id: '5418' relation: earlier_version status: public status: public title: Games with a weak adversary type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8573 year: '2014' ... --- _id: '5419' abstract: - lang: eng text: "We consider the reachability and shortest path problems on low tree-width graphs, with n nodes, m edges, and tree-width t, on a standard RAM with wordsize W. We use O to hide polynomial factors of the inverse of the Ackermann function. Our main contributions are three fold:\r\n1. For reachability, we present an algorithm that requires O(n·t2·log(n/t)) preprocessing time, O(n·(t·log(n/t))/W) space, and O(t/W) time for pair queries and O((n·t)/W) time for single-source queries. Note that for constant t our algorithm uses O(n·logn) time for preprocessing; and O(n/W) time for single-source queries, which is faster than depth first search/breath first search (after the preprocessing).\r\n2. We present an algorithm for shortest path that requires O(n·t2) preprocessing time, O(n·t) space, and O(t2) time for pair queries and O(n·t) time single-source queries.\r\n3. We give a space versus query time trade-off algorithm for shortest path that, given any constant >0, requires O(n·t2) preprocessing time, O(n·t2) space, and O(n1−·t2) time for pair queries.\r\nOur algorithms improve all existing results, and use very simple data structures." alternative_title: - IST Austria Technical Report 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: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-187-v1-1 apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Improved algorithms for reachability and shortest path on low tree-width graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-187-v1-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-187-v1-1. ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Improved algorithms for reachability and shortest path on low tree-width graphs. IST Austria, 2014. ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Improved algorithms for reachability and shortest path on low tree-width graphs, IST Austria, 34p. mla: Chatterjee, Krishnendu, et al. Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-187-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Improved Algorithms for Reachability and Shortest Path on Low Tree-Width Graphs, IST Austria, 2014. date_created: 2018-12-12T11:39:13Z date_published: 2014-04-14T00:00:00Z date_updated: 2021-01-12T08:02:03Z day: '14' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2014-187-v1-1 file: - access_level: open_access checksum: c608e66030a4bf51d2d99b451f539b99 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:25Z date_updated: 2020-07-14T12:46:50Z file_id: '5548' file_name: IST-2014-187-v1+1_main_full_tech.pdf file_size: 670031 relation: main_file file_date_updated: 2020-07-14T12:46:50Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '34' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '187' status: public title: Improved algorithms for reachability and shortest path on low tree-width graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '2217' abstract: - lang: eng text: "As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.\r\n\r\nThe contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem." acknowledgement: "This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/171" article_processing_charge: No author: - 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: 'Henzinger TA, Otop J. Model measuring for hybrid systems. In: Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control. Springer; 2014:213-222. doi:10.1145/2562059.2562130' apa: 'Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems. In Proceedings of the 17th international conference on Hybrid systems: computation and control (pp. 213–222). Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562130' chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Hybrid Systems.” In Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, 213–22. Springer, 2014. https://doi.org/10.1145/2562059.2562130.' ieee: 'T. A. Henzinger and J. Otop, “Model measuring for hybrid systems,” in Proceedings of the 17th international conference on Hybrid systems: computation and control, Berlin, Germany, 2014, pp. 213–222.' ista: 'Henzinger TA, Otop J. 2014. Model measuring for hybrid systems. Proceedings of the 17th international conference on Hybrid systems: computation and control. HSCC: Hybrid Systems - Computation and Control, 213–222.' mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Hybrid Systems.” Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–22, doi:10.1145/2562059.2562130.' short: 'T.A. Henzinger, J. Otop, in:, Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–222.' conference: end_date: 2014-04-17 location: Berlin, Germany name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2014-04-15 date_created: 2018-12-11T11:56:23Z date_published: 2014-04-01T00:00:00Z date_updated: 2023-02-23T12:25:23Z day: '01' department: - _id: ToHe doi: 10.1145/2562059.2562130 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 213 - 222 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: 'Proceedings of the 17th international conference on Hybrid systems: computation and control' publication_status: published publisher: Springer publist_id: '4751' quality_controlled: '1' related_material: record: - id: '5416' relation: earlier_version status: public scopus_import: 1 status: public title: Model measuring for hybrid systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5417' abstract: - lang: eng text: "We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M'within distance ρ from M satisfy (or violate)φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata.\r\nThe model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification.\r\nWe show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved.\r\nWe use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. \r\nWe give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications." alternative_title: - IST Austria Technical Report author: - 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: Henzinger TA, Otop J. From Model Checking to Model Measuring. IST Austria; 2014. doi:10.15479/AT:IST-2014-172-v1-1 apa: Henzinger, T. A., & Otop, J. (2014). From model checking to model measuring. IST Austria. https://doi.org/10.15479/AT:IST-2014-172-v1-1 chicago: Henzinger, Thomas A, and Jan Otop. From Model Checking to Model Measuring. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-172-v1-1. ieee: T. A. Henzinger and J. Otop, From model checking to model measuring. IST Austria, 2014. ista: Henzinger TA, Otop J. 2014. From model checking to model measuring, IST Austria, 14p. mla: Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring. IST Austria, 2014, doi:10.15479/AT:IST-2014-172-v1-1. short: T.A. Henzinger, J. Otop, From Model Checking to Model Measuring, IST Austria, 2014. date_created: 2018-12-12T11:39:13Z date_published: 2014-02-19T00:00:00Z date_updated: 2023-02-23T10:38:10Z day: '19' ddc: - '000' department: - _id: ToHe doi: 10.15479/AT:IST-2014-172-v1-1 file: - access_level: open_access checksum: fcc3eab903cfcd3778b338d2d0d44d18 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:20Z date_updated: 2020-07-14T12:46:49Z file_id: '5481' file_name: IST-2014-172-v1+1_report.pdf file_size: 383052 relation: main_file file_date_updated: 2020-07-14T12:46:49Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '14' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '175' related_material: record: - id: '2327' relation: later_version status: public status: public title: From model checking to model measuring type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5416' abstract: - lang: eng text: As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.The contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem. alternative_title: - IST Austria Technical Report author: - 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: Henzinger TA, Otop J. Model Measuring for Hybrid Systems. IST Austria; 2014. doi:10.15479/AT:IST-2014-171-v1-1 apa: Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems. IST Austria. https://doi.org/10.15479/AT:IST-2014-171-v1-1 chicago: Henzinger, Thomas A, and Jan Otop. Model Measuring for Hybrid Systems. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-171-v1-1. ieee: T. A. Henzinger and J. Otop, Model measuring for hybrid systems. IST Austria, 2014. ista: Henzinger TA, Otop J. 2014. Model measuring for hybrid systems, IST Austria, 22p. mla: Henzinger, Thomas A., and Jan Otop. Model Measuring for Hybrid Systems. IST Austria, 2014, doi:10.15479/AT:IST-2014-171-v1-1. short: T.A. Henzinger, J. Otop, Model Measuring for Hybrid Systems, IST Austria, 2014. date_created: 2018-12-12T11:39:12Z date_published: 2014-02-19T00:00:00Z date_updated: 2023-02-23T10:33:21Z day: '19' ddc: - '005' department: - _id: ToHe doi: 10.15479/AT:IST-2014-171-v1-1 file: - access_level: open_access checksum: 445456d22371e4e49aad2b9a0c13bf80 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:32Z date_updated: 2020-07-14T12:46:49Z file_id: '5492' file_name: IST-2014-171-v1+1_report.pdf file_size: 712077 relation: main_file file_date_updated: 2020-07-14T12:46:49Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '22' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '171' related_material: record: - id: '2217' relation: later_version status: public status: public title: Model measuring for hybrid systems type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5418' abstract: - lang: eng text: We consider multi-player graph games with partial-observation and parity objective. While the decision problem for three-player games with a coalition of the first and second players against the third player is undecidable, we present a decidability result for partial-observation games where the first and third player are in a coalition against the second player, thus where the second player is adversarial but weaker due to partial-observation. We establish tight complexity bounds in the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness for parity objectives. The symmetric case of player 1 more informed than player 2 is much more complicated, and we show that already in the case where player 1 has perfect observation, memory of size non-elementary is necessary in general for reachability objectives, and the problem is decidable for safety and reachability objectives. Our results have tight connections with partial-observation stochastic games for which we derive new complexity results. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen citation: ama: Chatterjee K, Doyen L. Games with a Weak Adversary. IST Austria; 2014. doi:10.15479/AT:IST-2014-176-v1-1 apa: Chatterjee, K., & Doyen, L. (2014). Games with a weak adversary. IST Austria. https://doi.org/10.15479/AT:IST-2014-176-v1-1 chicago: Chatterjee, Krishnendu, and Laurent Doyen. Games with a Weak Adversary. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-176-v1-1. ieee: K. Chatterjee and L. Doyen, Games with a weak adversary. IST Austria, 2014. ista: Chatterjee K, Doyen L. 2014. Games with a weak adversary, IST Austria, 18p. mla: Chatterjee, Krishnendu, and Laurent Doyen. Games with a Weak Adversary. IST Austria, 2014, doi:10.15479/AT:IST-2014-176-v1-1. short: K. Chatterjee, L. Doyen, Games with a Weak Adversary, IST Austria, 2014. date_created: 2018-12-12T11:39:13Z date_published: 2014-03-22T00:00:00Z date_updated: 2023-02-23T10:30:58Z day: '22' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2014-176-v1-1 file: - access_level: open_access checksum: 1d6958aa60050e1c3e932c6e5f34c39f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:07Z date_updated: 2020-07-14T12:46:49Z file_id: '5468' file_name: IST-2014-176-v1+1_icalp_14.pdf file_size: 328253 relation: main_file file_date_updated: 2020-07-14T12:46:49Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '18' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '176' related_material: record: - id: '2163' relation: later_version status: public status: public title: Games with a weak adversary type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5420' abstract: - lang: eng text: 'We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).' alternative_title: - IST Austria Technical Report 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 citation: ama: Chatterjee K, Ibsen-Jensen R. The Value 1 Problem for Concurrent Mean-Payoff Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-191-v1-1 apa: Chatterjee, K., & Ibsen-Jensen, R. (2014). The value 1 problem for concurrent mean-payoff games. IST Austria. https://doi.org/10.15479/AT:IST-2014-191-v1-1 chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem for Concurrent Mean-Payoff Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-191-v1-1. ieee: K. Chatterjee and R. Ibsen-Jensen, The value 1 problem for concurrent mean-payoff games. IST Austria, 2014. ista: Chatterjee K, Ibsen-Jensen R. 2014. The value 1 problem for concurrent mean-payoff games, IST Austria, 49p. mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Value 1 Problem for Concurrent Mean-Payoff Games. IST Austria, 2014, doi:10.15479/AT:IST-2014-191-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, The Value 1 Problem for Concurrent Mean-Payoff Games, IST Austria, 2014. date_created: 2018-12-12T11:39:14Z date_published: 2014-04-14T00:00:00Z date_updated: 2021-01-12T08:02:05Z day: '14' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2014-191-v1-1 file: - access_level: open_access checksum: 49e0fd3e62650346daf7dc04604f7a0a content_type: application/pdf creator: system date_created: 2018-12-12T11:53:58Z date_updated: 2020-07-14T12:46:50Z file_id: '5520' file_name: IST-2014-191-v1+1_main_full.pdf file_size: 584368 relation: main_file file_date_updated: 2020-07-14T12:46:50Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '49' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '191' status: public title: The value 1 problem for concurrent mean-payoff games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5422' abstract: - lang: eng text: Notes from the Third Plenary for the Research Data Alliance in Dublin, Ireland on March 26 to 28, 2014 with focus on starting an institutional research data repository. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none; 2014. apa: Porsche, J. (2014). Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none. chicago: Porsche, Jana. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none, 2014. ieee: J. Porsche, Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none, 2014. ista: Porsche J. 2014. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland, none,p. mla: Porsche, Jana. Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland. none, 2014. short: J. Porsche, Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland, none, 2014. date_created: 2018-12-12T11:39:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2020-07-14T23:04:56Z ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: 3954896648ce8afa8f7c4425e71cff08 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:40Z date_updated: 2020-07-14T12:46:50Z file_id: '5501' file_name: IST-2014-254-v1+1_Dublin_Day_3.pdf file_size: 648585 relation: main_file - access_level: open_access checksum: 9a0d42b0b832dfe7e4b22fb6816bcbba content_type: application/pdf creator: system date_created: 2018-12-12T11:53:41Z date_updated: 2020-07-14T12:46:50Z file_id: '5502' file_name: IST-2014-254-v1+2_Dublin_Day_1.pdf file_size: 221339 relation: main_file - access_level: open_access checksum: 498b8d629fb1bd17bff1dc43700a93e6 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:42Z date_updated: 2020-07-14T12:46:50Z file_id: '5503' file_name: IST-2014-254-v1+3_Dublin_Day_2.pdf file_size: 187778 relation: main_file file_date_updated: 2020-07-14T12:46:50Z has_accepted_license: '1' language: - iso: eng oa: 1 oa_version: None publisher: none pubrep_id: '254' status: public title: Notes from Research Data Alliance Plenary Meeting in Dublin, Ireland type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5424' abstract: - lang: eng text: We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty. alternative_title: - IST Austria Technical Report author: - 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: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Raghav full_name: Gupta, Raghav last_name: Gupta - first_name: Ayush full_name: Kanodia, Ayush last_name: Kanodia citation: ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria; 2014. doi:10.15479/AT:IST-2014-305-v1-1 apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v1-1 chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v1-1. ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria, 2014. ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications, IST Austria, 12p. mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v1-1. short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria, 2014. date_created: 2018-12-12T11:39:15Z date_published: 2014-09-09T00:00:00Z date_updated: 2023-02-23T12:25:52Z day: '09' ddc: - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2014-305-v1-1 file: - access_level: open_access checksum: 35009d5fad01198341e6c1a3353481b7 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:51Z date_updated: 2020-07-14T12:46:51Z file_id: '5512' file_name: IST-2014-305-v1+1_main.pdf file_size: 655774 relation: main_file file_date_updated: 2020-07-14T12:46:51Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '12' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '305' related_material: record: - id: '1732' relation: later_version status: public - id: '5426' relation: later_version status: public status: public title: Qualitative analysis of POMDPs with temporal logic specifications for robotics applications type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5426' abstract: - lang: eng text: We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty. alternative_title: - IST Austria Technical Report author: - 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: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Raghav full_name: Gupta, Raghav last_name: Gupta - first_name: Ayush full_name: Kanodia, Ayush last_name: Kanodia citation: ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria; 2014. doi:10.15479/AT:IST-2014-305-v2-1 apa: Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2014). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria. https://doi.org/10.15479/AT:IST-2014-305-v2-1 chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-305-v2-1. ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. IST Austria, 2014. ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2014. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications, IST Austria, 10p. mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IST Austria, 2014, doi:10.15479/AT:IST-2014-305-v2-1. short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications, IST Austria, 2014. date_created: 2018-12-12T11:39:16Z date_published: 2014-09-29T00:00:00Z date_updated: 2023-02-23T12:25:47Z day: '29' ddc: - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2014-305-v2-1 file: - access_level: open_access checksum: 730c0a8e97cf2712a884b2cc423f3919 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:15Z date_updated: 2020-07-14T12:46:51Z file_id: '5537' file_name: IST-2014-305-v2+1_main2.pdf file_size: 656019 relation: main_file file_date_updated: 2020-07-14T12:46:51Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '10' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '311' related_material: record: - id: '1732' relation: later_version status: public - id: '5424' relation: earlier_version status: public status: public title: Qualitative analysis of POMDPs with temporal logic specifications for robotics applications type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5423' abstract: - lang: eng text: 'We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm- deadline real-time tasks based on multi-objective graphs: Given a taskset and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. a clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including D(over), that have been proposed in the past, for various tasksets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are tasksets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application. ' alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Alexander full_name: Kössler, Alexander last_name: Kössler - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Ulrich full_name: Schmid, Ulrich last_name: Schmid citation: ama: Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria; 2014. doi:10.15479/AT:IST-2014-300-v1-1 apa: Chatterjee, K., Kössler, A., Pavlogiannis, A., & Schmid, U. (2014). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. IST Austria. https://doi.org/10.15479/AT:IST-2014-300-v1-1 chicago: Chatterjee, Krishnendu, Alexander Kössler, Andreas Pavlogiannis, and Ulrich Schmid. A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-300-v1-1. ieee: K. Chatterjee, A. Kössler, A. Pavlogiannis, and U. Schmid, A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. IST Austria, 2014. ista: Chatterjee K, Kössler A, Pavlogiannis A, Schmid U. 2014. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks, IST Austria, 14p. mla: Chatterjee, Krishnendu, et al. A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks. IST Austria, 2014, doi:10.15479/AT:IST-2014-300-v1-1. short: K. Chatterjee, A. Kössler, A. Pavlogiannis, U. Schmid, A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks, IST Austria, 2014. date_created: 2018-12-12T11:39:15Z date_published: 2014-07-29T00:00:00Z date_updated: 2023-02-23T10:11:15Z day: '29' ddc: - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2014-300-v1-1 file: - access_level: open_access checksum: 4b8fde4d9ef6653837f6803921d83032 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:53Z date_updated: 2020-07-14T12:46:50Z file_id: '5514' file_name: IST-2014-300-v1+1_main.pdf file_size: 1270021 relation: main_file file_date_updated: 2020-07-14T12:46:50Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '14' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '300' related_material: record: - id: '1714' relation: later_version status: public status: public title: A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5427' abstract: - lang: eng text: 'We consider graphs with n nodes together with their tree-decomposition that has b = O ( n ) bags and width t , on the standard RAM computational model with wordsize W = Θ (log n ) . Our contributions are two-fold: Our first contribution is an algorithm that given a graph and its tree-decomposition as input, computes a binary and balanced tree-decomposition of width at most 4 · t + 3 of the graph in O ( b ) time and space, improving a long-standing (from 1992) bound of O ( n · log n ) time for constant treewidth graphs. Our second contribution is on reachability queries for low treewidth graphs. We build on our tree-balancing algorithm and present a data-structure for graph reachability that requires O ( n · t 2 ) preprocessing time, O ( n · t ) space, and O ( d t/ log n e ) time for pair queries, and O ( n · t · log t/ log n ) time for single-source queries. For constant t our data-structure uses O ( n ) time for preprocessing, O (1) time for pair queries, and O ( n/ log n ) time for single-source queries. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries.' alternative_title: - IST Austria Technical Report 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: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-314-v1-1 apa: Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2014). Optimal tree-decomposition balancing and reachability on low treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-314-v1-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-314-v1-1. ieee: K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Optimal tree-decomposition balancing and reachability on low treewidth graphs. IST Austria, 2014. ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Optimal tree-decomposition balancing and reachability on low treewidth graphs, IST Austria, 24p. mla: Chatterjee, Krishnendu, et al. Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-314-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs, IST Austria, 2014. date_created: 2018-12-12T11:39:16Z date_published: 2014-11-05T00:00:00Z date_updated: 2021-01-12T08:02:09Z day: '05' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2014-314-v1-1 file: - access_level: open_access checksum: 9d3b90bf4fff74664f182f2d95ef727a content_type: application/pdf creator: system date_created: 2018-12-12T11:53:10Z date_updated: 2020-07-14T12:46:52Z file_id: '5471' file_name: IST-2014-314-v1+1_long.pdf file_size: 405561 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '24' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '314' status: public title: Optimal tree-decomposition balancing and reachability on low treewidth graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5425' abstract: - lang: eng text: ' We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objective we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest.' alternative_title: - IST Austria Technical Report author: - first_name: '1' full_name: Anonymous, 1 last_name: Anonymous - first_name: '2' full_name: Anonymous, 2 last_name: Anonymous - first_name: '3' full_name: Anonymous, 3 last_name: Anonymous - first_name: '4' full_name: Anonymous, 4 last_name: Anonymous citation: ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Optimal Cost Almost-Sure Reachability in POMDPs. IST Austria; 2014. apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2014). Optimal cost almost-sure reachability in POMDPs. IST Austria. chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Optimal Cost Almost-Sure Reachability in POMDPs. IST Austria, 2014. ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Optimal cost almost-sure reachability in POMDPs. IST Austria, 2014. ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2014. Optimal cost almost-sure reachability in POMDPs, IST Austria, 22p. mla: Anonymous, 1, et al. Optimal Cost Almost-Sure Reachability in POMDPs. IST Austria, 2014. short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Optimal Cost Almost-Sure Reachability in POMDPs, IST Austria, 2014. date_created: 2018-12-12T11:39:15Z date_published: 2014-09-09T00:00:00Z date_updated: 2023-02-23T10:02:57Z day: '09' ddc: - '000' file: - access_level: open_access checksum: b9668a70d53c550b3cd64f0c77451c3d content_type: application/pdf creator: system date_created: 2018-12-12T11:53:17Z date_updated: 2020-07-14T12:46:51Z file_id: '5478' file_name: IST-2014-307-v1+1_main.pdf file_size: 2725429 relation: main_file - access_level: closed checksum: 808ada1dddecc48ca041526fcc6a9efd content_type: text/plain creator: dernst date_created: 2019-04-16T14:16:12Z date_updated: 2020-07-14T12:46:51Z file_id: '6322' file_name: IST-2014-307-v1+2_authors.txt file_size: 117 relation: main_file file_date_updated: 2020-07-14T12:46:51Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '22' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '307' related_material: record: - id: '1529' relation: later_version status: public scopus_import: 1 status: public title: Optimal cost almost-sure reachability in POMDPs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5415' abstract: - lang: eng text: 'Recently there has been a significant effort to add 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, several basic system properties such as average response time cannot be expressed with weighted automata. In this work, we introduce nested weighted automata as a new formalism for expressing important quantitative properties such as average response time. We establish an almost complete decidability picture for the basic decision problems for nested weighted automata, and illustrate its applicability in several domains. ' alternative_title: - IST Austria Technical Report 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. IST Austria; 2014. doi:10.15479/AT:IST-2014-170-v1-1 apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2014). Nested weighted automata. IST Austria. https://doi.org/10.15479/AT:IST-2014-170-v1-1 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted Automata. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-170-v1-1. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata. IST Austria, 2014. ista: Chatterjee K, Henzinger TA, Otop J. 2014. Nested weighted automata, IST Austria, 27p. mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria, 2014, doi:10.15479/AT:IST-2014-170-v1-1. short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2014. date_created: 2018-12-12T11:39:12Z date_published: 2014-02-19T00:00:00Z date_updated: 2023-02-23T12:26:19Z day: '19' ddc: - '004' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2014-170-v1-1 file: - access_level: open_access checksum: 31f90dcf2cf899c3f8c6427cfcc2b3c7 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:36Z date_updated: 2020-07-14T12:46:48Z file_id: '5497' file_name: IST-2014-170-v1+1_main.pdf file_size: 573457 relation: main_file file_date_updated: 2020-07-14T12:46:48Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '27' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '170' related_material: record: - id: '1656' relation: later_version status: public - id: '467' relation: later_version status: public - id: '5436' relation: later_version status: public status: public title: Nested weighted automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5421' abstract: - lang: eng text: 'Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are: (1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure). (2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.' alternative_title: - IST Austria Technical Report 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. The Complexity of Evolution on Graphs. IST Austria; 2014. doi:10.15479/AT:IST-2014-190-v2-2 apa: Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2014). The complexity of evolution on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2014-190-v2-2 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolution on Graphs. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-190-v2-2. ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolution on graphs. IST Austria, 2014. ista: Chatterjee K, Ibsen-Jensen R, Nowak M. 2014. The complexity of evolution on graphs, IST Austria, 27p. mla: Chatterjee, Krishnendu, et al. The Complexity of Evolution on Graphs. IST Austria, 2014, doi:10.15479/AT:IST-2014-190-v2-2. short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolution on Graphs, IST Austria, 2014. date_created: 2018-12-12T11:39:14Z date_published: 2014-04-18T00:00:00Z date_updated: 2023-02-23T12:26:33Z day: '18' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2014-190-v2-2 file: - access_level: open_access checksum: 42f3d8b563286eb0d903832bd9a848d3 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:16Z date_updated: 2020-07-14T12:46:50Z file_id: '5538' file_name: IST-2014-190-v2+2_main_full.pdf file_size: 443529 relation: main_file - access_level: open_access checksum: 0c9a2fd822309719634495a35957e34d content_type: application/pdf creator: kschuh date_created: 2019-09-06T07:30:20Z date_updated: 2020-07-14T12:46:50Z file_id: '6852' file_name: IST-2014-190-v1+1_main_full.pdf file_size: 440911 relation: main_file file_date_updated: 2020-07-14T12:46:50Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '27' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '190' related_material: record: - id: '5432' relation: later_version status: public - id: '5440' relation: later_version status: public status: public title: The complexity of evolution on graphs type: technical_report user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '5813' abstract: - lang: eng text: We consider homogeneous Bose gas in a large cubic box with periodic boundary conditions, at zero temperature. We analyze its excitation spectrum in a certain kind of a mean-field infinite-volume limit. We prove that under appropriate conditions the excitation spectrum has the form predicted by the Bogoliubov approximation. Our result can be viewed as an extension of the result of Seiringer (Commun. Math. Phys.306:565–578, 2011) to large volumes. article_processing_charge: No author: - first_name: Jan full_name: Dereziński, Jan last_name: Dereziński - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski citation: ama: Dereziński J, Napiórkowski MM. Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. 2014;15(12):2409-2439. doi:10.1007/s00023-013-0302-4 apa: Dereziński, J., & Napiórkowski, M. M. (2014). Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. Springer Nature. https://doi.org/10.1007/s00023-013-0302-4 chicago: Dereziński, Jan, and Marcin M Napiórkowski. “Excitation Spectrum of Interacting Bosons in the Mean-Field Infinite-Volume Limit.” Annales Henri Poincaré. Springer Nature, 2014. https://doi.org/10.1007/s00023-013-0302-4. ieee: J. Dereziński and M. M. Napiórkowski, “Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit,” Annales Henri Poincaré, vol. 15, no. 12. Springer Nature, pp. 2409–2439, 2014. ista: Dereziński J, Napiórkowski MM. 2014. Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. 15(12), 2409–2439. mla: Dereziński, Jan, and Marcin M. Napiórkowski. “Excitation Spectrum of Interacting Bosons in the Mean-Field Infinite-Volume Limit.” Annales Henri Poincaré, vol. 15, no. 12, Springer Nature, 2014, pp. 2409–39, doi:10.1007/s00023-013-0302-4. short: J. Dereziński, M.M. Napiórkowski, Annales Henri Poincaré 15 (2014) 2409–2439. date_created: 2019-01-10T09:02:58Z date_published: 2014-01-10T00:00:00Z date_updated: 2021-11-16T08:13:24Z day: '10' ddc: - '530' doi: 10.1007/s00023-013-0302-4 extern: '1' file: - access_level: open_access checksum: 1f6c32c5d6ec90cdb0718c7f0103342e content_type: application/pdf creator: dernst date_created: 2019-01-10T09:04:45Z date_updated: 2020-07-14T12:47:11Z file_id: '5814' file_name: 2014_Annales_Derezinski.pdf file_size: 865230 relation: main_file file_date_updated: 2020-07-14T12:47:11Z has_accepted_license: '1' intvolume: ' 15' issue: '12' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 2409-2439 publication: Annales Henri Poincaré publication_identifier: issn: - 1424-0637 - 1424-0661 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1007/s00023-014-0390-9 status: public title: Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit 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: 15 year: '2014' ... --- _id: '5810' abstract: - lang: eng text: A discrete spherical geodesic path between two voxels s and t lying on a discrete sphere is a/the 1-connected shortest path from s to t, comprising voxels of the discrete sphere intersected by the real plane passing through s, t, and the center of the sphere. We show that the set of sphere voxels intersected by the aforesaid real plane always contains a 1-connected cycle passing through s and t, and each voxel in this set lies within an isothetic distance of 32 from the concerned plane. Hence, to compute the path, the algorithm starts from s, and iteratively computes each voxel p of the path from the predecessor of p. A novel number-theoretic property and the 48-symmetry of discrete sphere are used for searching the 1-connected voxels comprising the path. The algorithm is output-sensitive, having its time and space complexities both linear in the length of the path. It can be extended for constructing 1-connected discrete 3D circles of arbitrary orientations, specified by a few appropriate input parameters. Experimental results and related analysis demonstrate its efficiency and versatility. 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 Finding Spherical Geodesic Paths and Circles in ℤ3. 2014;8668:396-409. doi:10.1007/978-3-319-09955-2_33 apa: 'Biswas, R., & Bhowmick, P. (2014). On Finding Spherical Geodesic Paths and Circles in ℤ3. Presented at the DGCI: International Conference on Discrete Geometry for Computer Imagery, Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-319-09955-2_33' chicago: 'Biswas, Ranita, and Partha Bhowmick. “On Finding Spherical Geodesic Paths and Circles in ℤ3.” Lecture Notes in Computer Science. Berlin, Heidelberg: Springer, 2014. https://doi.org/10.1007/978-3-319-09955-2_33.' ieee: R. Biswas and P. Bhowmick, “On Finding Spherical Geodesic Paths and Circles in ℤ3,” vol. 8668. Springer, Berlin, Heidelberg, pp. 396–409, 2014. ista: Biswas R, Bhowmick P. 2014. On Finding Spherical Geodesic Paths and Circles in ℤ3. 8668, 396–409. mla: Biswas, Ranita, and Partha Bhowmick. On Finding Spherical Geodesic Paths and Circles in ℤ3. Vol. 8668, Springer, 2014, pp. 396–409, doi:10.1007/978-3-319-09955-2_33. short: R. Biswas, P. Bhowmick, 8668 (2014) 396–409. conference: end_date: 2014-09-12 location: Siena, Italy name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery' start_date: 2014-09-10 date_created: 2019-01-08T20:45:32Z date_published: 2014-01-01T00:00:00Z date_updated: 2019-01-24T13:22:49Z doi: 10.1007/978-3-319-09955-2_33 extern: '1' intvolume: ' 8668' language: - iso: eng oa_version: None page: 396-409 place: Berlin, Heidelberg publication_identifier: isbn: - '9783642387081' - '9783642387098' issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer quality_controlled: '1' series_title: Lecture Notes in Computer Science status: public title: On Finding Spherical Geodesic Paths and Circles in ℤ3 type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8668 year: '2014' ... --- _id: '589' abstract: - lang: eng text: We demonstrate a many-atom-cavity system with a high-finesse dual-wavelength standing wave cavity in which all participating rubidium atoms are nearly identically coupled to a 780-nm cavity mode. This homogeneous coupling is enforced by a one-dimensional optical lattice formed by the field of a 1560-nm cavity mode. author: - first_name: Jongmin full_name: Lee, Jongmin last_name: Lee - first_name: Geert full_name: Vrijsen, Geert last_name: Vrijsen - first_name: Igor full_name: Teper, Igor last_name: Teper - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Mark full_name: Kasevich, Mark A last_name: Kasevich citation: ama: Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. Many-atom-cavity QED system with homogeneous atom-cavity coupling. Optics Letters. 2014;39(13):4005-4008. doi:10.1364/OL.39.004005 apa: Lee, J., Vrijsen, G., Teper, I., Hosten, O., & Kasevich, M. (2014). Many-atom-cavity QED system with homogeneous atom-cavity coupling. Optics Letters. OSA. https://doi.org/10.1364/OL.39.004005 chicago: Lee, Jongmin, Geert Vrijsen, Igor Teper, Onur Hosten, and Mark Kasevich. “Many-Atom-Cavity QED System with Homogeneous Atom-Cavity Coupling.” Optics Letters. OSA, 2014. https://doi.org/10.1364/OL.39.004005. ieee: J. Lee, G. Vrijsen, I. Teper, O. Hosten, and M. Kasevich, “Many-atom-cavity QED system with homogeneous atom-cavity coupling,” Optics Letters, vol. 39, no. 13. OSA, pp. 4005–4008, 2014. ista: Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. 2014. Many-atom-cavity QED system with homogeneous atom-cavity coupling. Optics Letters. 39(13), 4005–4008. mla: Lee, Jongmin, et al. “Many-Atom-Cavity QED System with Homogeneous Atom-Cavity Coupling.” Optics Letters, vol. 39, no. 13, OSA, 2014, pp. 4005–08, doi:10.1364/OL.39.004005. short: J. Lee, G. Vrijsen, I. Teper, O. Hosten, M. Kasevich, Optics Letters 39 (2014) 4005–4008. date_created: 2018-12-11T11:47:21Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T08:05:09Z day: '01' doi: 10.1364/OL.39.004005 extern: 1 intvolume: ' 39' issue: '13' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.1805 month: '07' oa: 1 page: 4005 - 4008 publication: Optics Letters publication_status: published publisher: OSA publist_id: '7216' quality_controlled: 0 status: public title: Many-atom-cavity QED system with homogeneous atom-cavity coupling type: journal_article volume: 39 year: '2014' ... --- _id: '6126' abstract: - lang: eng text: Aerobic animals constantly monitor and adapt to changes in O2 levels. The molecular mechanisms involved in sensing O2 are, however, incompletely understood. Previous studies showed that a hexacoordinated globin called GLB-5 tunes the dynamic range of O2-sensing neurons in natural C. elegans isolates, but is defective in the N2 lab reference strain (McGrath et al., 2009; Persson et al., 2009). GLB-5 enables a sharp behavioral switch when O2 changes between 21 and 17%. Here, we show that GLB-5 also confers rapid behavioral and cellular recovery from exposure to hypoxia. Hypoxia reconfigures O2-evoked Ca2+ responses in the URX O2 sensors, and GLB-5 enables rapid recovery of these responses upon re-oxygenation. Forward genetic screens indicate that GLB-5's effects on O2 sensing require PDL-1, the C. elegans ortholog of mammalian PrBP/PDE6δ protein. In mammals, PDE6δ regulates the traffic and activity of prenylated proteins (Zhang et al., 2004; Norton et al., 2005). PDL-1 promotes localization of GCY-33 and GCY-35, atypical soluble guanylate cyclases that act as O2 sensors, to the dendritic endings of URX and BAG neurons, where they colocalize with GLB-5. Both GCY-33 and GCY-35 are predicted to be prenylated. Dendritic localization is not essential for GCY-35 to function as an O2 sensor, but disrupting pdl-1 alters the URX neuron's O2 response properties. Functional GLB-5 can restore dendritic localization of GCY-33 in pdl-1 mutants, suggesting GCY-33 and GLB-5 are in a complex. Our data suggest GLB-5 and the soluble guanylate cyclases operate in close proximity to sculpt O2 responses. author: - first_name: E. full_name: Gross, E. last_name: Gross - first_name: Z. full_name: Soltesz, Z. last_name: Soltesz - first_name: S. full_name: Oda, S. last_name: Oda - first_name: V. full_name: Zelmanovich, V. last_name: Zelmanovich - first_name: Z. full_name: Abergel, Z. last_name: Abergel - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings. Journal of Neuroscience. 2014;34(50):16726-16738. doi:10.1523/jneurosci.5368-13.2014 apa: Gross, E., Soltesz, Z., Oda, S., Zelmanovich, V., Abergel, Z., & de Bono, M. (2014). GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.5368-13.2014 chicago: Gross, E., Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and Mario de Bono. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP That Targets Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” Journal of Neuroscience. Society for Neuroscience, 2014. https://doi.org/10.1523/jneurosci.5368-13.2014. ieee: E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and M. de Bono, “GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings,” Journal of Neuroscience, vol. 34, no. 50. Society for Neuroscience, pp. 16726–16738, 2014. ista: Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. 2014. GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings. Journal of Neuroscience. 34(50), 16726–16738. mla: Gross, E., et al. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP That Targets Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” Journal of Neuroscience, vol. 34, no. 50, Society for Neuroscience, 2014, pp. 16726–38, doi:10.1523/jneurosci.5368-13.2014. short: E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, M. de Bono, Journal of Neuroscience 34 (2014) 16726–16738. date_created: 2019-03-19T14:52:26Z date_published: 2014-12-10T00:00:00Z date_updated: 2021-01-12T08:06:14Z day: '10' ddc: - '570' doi: 10.1523/jneurosci.5368-13.2014 extern: '1' external_id: pmid: - '25505325' file: - access_level: open_access checksum: a3dd71969f94c43909327cd083283d4b content_type: application/pdf creator: kschuh date_created: 2019-03-19T14:55:58Z date_updated: 2020-07-14T12:47:20Z file_id: '6127' file_name: 2014_SFN_Gross.pdf file_size: 3263422 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 34' issue: '50' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 16726-16738 pmid: 1 publication: Journal of Neuroscience publication_identifier: issn: - 0270-6474 - 1529-2401 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' status: public title: GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings 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: 34 year: '2014' ... --- _id: '6124' abstract: - lang: eng text: Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4 and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene encodes a conserved tail-anchored transmembrane protein; the molecular identity of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4 also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding, maturation, or export from the ER. The physical interaction between human ODR4 and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues required for protease activity can rescue all odr-8 mutant phenotypes tested. Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia, either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and Ufm1-independent functions in GPCR biogenesis. article_number: e1004082 author: - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Eisuke full_name: Itakura, Eisuke last_name: Itakura - first_name: Katherine P. full_name: Weber, Katherine P. last_name: Weber - first_name: Ramanujan S. full_name: Hegde, Ramanujan S. last_name: Hegde - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. PLoS Genetics. 2014;10(3). doi:10.1371/journal.pgen.1004082 apa: Chen, C., Itakura, E., Weber, K. P., Hegde, R. S., & de Bono, M. (2014). An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. PLoS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004082 chicago: Chen, Changchun, Eisuke Itakura, Katherine P. Weber, Ramanujan S. Hegde, and Mario de Bono. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease 2 Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” PLoS Genetics. Public Library of Science (PLoS), 2014. https://doi.org/10.1371/journal.pgen.1004082. ieee: C. Chen, E. Itakura, K. P. Weber, R. S. Hegde, and M. de Bono, “An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism,” PLoS Genetics, vol. 10, no. 3. Public Library of Science (PLoS), 2014. ista: Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. 2014. An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. PLoS Genetics. 10(3), e1004082. mla: Chen, Changchun, et al. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease 2 Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” PLoS Genetics, vol. 10, no. 3, e1004082, Public Library of Science (PLoS), 2014, doi:10.1371/journal.pgen.1004082. short: C. Chen, E. Itakura, K.P. Weber, R.S. Hegde, M. de Bono, PLoS Genetics 10 (2014). date_created: 2019-03-19T14:45:56Z date_published: 2014-03-06T00:00:00Z date_updated: 2021-01-12T08:06:14Z day: '06' ddc: - '570' doi: 10.1371/journal.pgen.1004082 extern: '1' external_id: pmid: - '24603482' file: - access_level: open_access checksum: ac19941089a4262bb5bd74434a08b003 content_type: application/pdf creator: kschuh date_created: 2019-03-19T14:50:07Z date_updated: 2020-07-14T12:47:20Z file_id: '6125' file_name: 2014_PLOS_Chen.PDF file_size: 8286819 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 10' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science (PLoS) quality_controlled: '1' status: public title: An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism 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: 10 year: '2014' ... --- _id: '6122' author: - first_name: Gerit A. full_name: Linneweber, Gerit A. last_name: Linneweber - first_name: Jake full_name: Jacobson, Jake last_name: Jacobson - first_name: Karl Emanuel full_name: Busch, Karl Emanuel last_name: Busch - first_name: Bruno full_name: Hudry, Bruno last_name: Hudry - first_name: Christo P. full_name: Christov, Christo P. last_name: Christov - first_name: Dirk full_name: Dormann, Dirk last_name: Dormann - first_name: Michaela full_name: Yuan, Michaela last_name: Yuan - first_name: Tomoki full_name: Otani, Tomoki last_name: Otani - first_name: Elisabeth full_name: Knust, Elisabeth last_name: Knust - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Irene full_name: Miguel-Aliaga, Irene last_name: Miguel-Aliaga citation: ama: Linneweber GA, Jacobson J, Busch KE, et al. Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching. Cell. 2014;156(1-2):69-83. doi:10.1016/j.cell.2013.12.008 apa: Linneweber, G. A., Jacobson, J., Busch, K. E., Hudry, B., Christov, C. P., Dormann, D., … Miguel-Aliaga, I. (2014). Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.12.008 chicago: Linneweber, Gerit A., Jake Jacobson, Karl Emanuel Busch, Bruno Hudry, Christo P. Christov, Dirk Dormann, Michaela Yuan, et al. “Neuronal Control of Metabolism through Nutrient-Dependent Modulation of Tracheal Branching.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2013.12.008. ieee: G. A. Linneweber et al., “Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching,” Cell, vol. 156, no. 1–2. Elsevier, pp. 69–83, 2014. ista: Linneweber GA, Jacobson J, Busch KE, Hudry B, Christov CP, Dormann D, Yuan M, Otani T, Knust E, de Bono M, Miguel-Aliaga I. 2014. Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching. Cell. 156(1–2), 69–83. mla: Linneweber, Gerit A., et al. “Neuronal Control of Metabolism through Nutrient-Dependent Modulation of Tracheal Branching.” Cell, vol. 156, no. 1–2, Elsevier, 2014, pp. 69–83, doi:10.1016/j.cell.2013.12.008. short: G.A. Linneweber, J. Jacobson, K.E. Busch, B. Hudry, C.P. Christov, D. Dormann, M. Yuan, T. Otani, E. Knust, M. de Bono, I. Miguel-Aliaga, Cell 156 (2014) 69–83. date_created: 2019-03-19T14:35:30Z date_published: 2014-01-16T00:00:00Z date_updated: 2021-01-12T08:06:13Z day: '16' ddc: - '570' doi: 10.1016/j.cell.2013.12.008 extern: '1' external_id: pmid: - '24439370' file: - access_level: open_access checksum: ad6ef68f37fb711d9abcd97fc06ad316 content_type: application/pdf creator: kschuh date_created: 2019-03-19T14:40:38Z date_updated: 2020-07-14T12:47:20Z file_id: '6123' file_name: 2014_Elsevier_Linneweber.pdf file_size: 5020084 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 156' issue: 1-2 language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 69-83 pmid: 1 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching 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: 156 year: '2014' ... --- _id: '6319' abstract: - lang: fre text: Nous étudions le comportement asymptotique du nombre de variétés dans une certaine classe ne satisfaisant pas le principe de Hasse. Cette étude repose sur des résultats récemmentobtenus par Colliot-Thélène. author: - first_name: Régis de la full_name: Bretèche, Régis de la last_name: Bretèche - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Bretèche R de la, Browning TD. Contre-exemples au principe de Hasse pour certains tores coflasques. Journal de Théorie des Nombres de Bordeaux. 2014;26(1):25-44. doi:10.5802/jtnb.857 apa: Bretèche, R. de la, & Browning, T. D. (2014). Contre-exemples au principe de Hasse pour certains tores coflasques. Journal de Théorie Des Nombres de Bordeaux. Cellule MathDoc/CEDRAM. https://doi.org/10.5802/jtnb.857 chicago: Bretèche, Régis de la, and Timothy D Browning. “Contre-Exemples Au Principe de Hasse Pour Certains Tores Coflasques.” Journal de Théorie Des Nombres de Bordeaux. Cellule MathDoc/CEDRAM, 2014. https://doi.org/10.5802/jtnb.857. ieee: R. de la Bretèche and T. D. Browning, “Contre-exemples au principe de Hasse pour certains tores coflasques,” Journal de Théorie des Nombres de Bordeaux, vol. 26, no. 1. Cellule MathDoc/CEDRAM, pp. 25–44, 2014. ista: Bretèche R de la, Browning TD. 2014. Contre-exemples au principe de Hasse pour certains tores coflasques. Journal de Théorie des Nombres de Bordeaux. 26(1), 25–44. mla: Bretèche, Régis de la, and Timothy D. Browning. “Contre-Exemples Au Principe de Hasse Pour Certains Tores Coflasques.” Journal de Théorie Des Nombres de Bordeaux, vol. 26, no. 1, Cellule MathDoc/CEDRAM, 2014, pp. 25–44, doi:10.5802/jtnb.857. short: R. de la Bretèche, T.D. Browning, Journal de Théorie Des Nombres de Bordeaux 26 (2014) 25–44. date_created: 2019-04-16T13:40:13Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:07:03Z doi: 10.5802/jtnb.857 extern: '1' external_id: arxiv: - '1210.4236' intvolume: ' 26' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1210.4236 oa: 1 oa_version: Preprint page: 25-44 publication: Journal de Théorie des Nombres de Bordeaux publication_identifier: issn: - 1246-7405 - 2118-8572 publication_status: published publisher: Cellule MathDoc/CEDRAM quality_controlled: '1' status: public title: Contre-exemples au principe de Hasse pour certains tores coflasques type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '6740' abstract: - lang: eng text: We describe coding techniques that achieve the capacity of a discrete memoryless asymmetric channel. To do so, we discuss how recent advances in coding for symmetric channels yield more efficient solutions also for the asymmetric case. In more detail, we consider three basic approaches. The first one is Gallager's scheme that concatenates a linear code with a non-linear mapper, in order to bias the input distribution. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Further, we derive a scaling law between the gap to capacity, the cardinality of channel input and output alphabets, and the required size of the mapper. The second one is an integrated approach in which the coding scheme is used both for source coding, in order to create codewords with the capacity-achieving distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third approach is based on an idea due to Böcherer and Mathar and separates completely the two tasks of source coding and channel coding by “chaining” together several codewords. We prove that we can combine any suitable source code with any suitable channel code in order to provide optimal schemes for asymmetric channels. In particular, polar codes and spatially coupled codes fulfill the required conditions. author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani citation: ama: 'Mondelli M, Urbanke R, Hassani H. How to achieve the capacity of asymmetric channels. In: 52nd Annual Allerton Conference on Communication, Control, and Computing. IEEE; 2014:789-796. doi:10.1109/allerton.2014.7028535' apa: 'Mondelli, M., Urbanke, R., & Hassani, H. (2014). How to achieve the capacity of asymmetric channels. In 52nd Annual Allerton Conference on Communication, Control, and Computing (pp. 789–796). Monticello, IL, United States: IEEE. https://doi.org/10.1109/allerton.2014.7028535' chicago: Mondelli, Marco, Rudiger Urbanke, and Hamed Hassani. “How to Achieve the Capacity of Asymmetric Channels.” In 52nd Annual Allerton Conference on Communication, Control, and Computing, 789–96. IEEE, 2014. https://doi.org/10.1109/allerton.2014.7028535. ieee: M. Mondelli, R. Urbanke, and H. Hassani, “How to achieve the capacity of asymmetric channels,” in 52nd Annual Allerton Conference on Communication, Control, and Computing, Monticello, IL, United States, 2014, pp. 789–796. ista: Mondelli M, Urbanke R, Hassani H. 2014. How to achieve the capacity of asymmetric channels. 52nd Annual Allerton Conference on Communication, Control, and Computing. Allerton Conference on Communication, Control, and Computing, 789–796. mla: Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” 52nd Annual Allerton Conference on Communication, Control, and Computing, IEEE, 2014, pp. 789–96, doi:10.1109/allerton.2014.7028535. short: M. Mondelli, R. Urbanke, H. Hassani, in:, 52nd Annual Allerton Conference on Communication, Control, and Computing, IEEE, 2014, pp. 789–796. conference: end_date: 2014-10-03 location: Monticello, IL, United States name: Allerton Conference on Communication, Control, and Computing start_date: 2014-09-30 date_created: 2019-07-31T07:24:23Z date_published: 2014-10-01T00:00:00Z date_updated: 2023-02-23T12:49:36Z day: '01' doi: 10.1109/allerton.2014.7028535 extern: '1' external_id: arxiv: - '1406.7373' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1406.7373 month: '10' oa: 1 oa_version: Preprint page: 789-796 publication: 52nd Annual Allerton Conference on Communication, Control, and Computing publication_identifier: eisbn: - 978-1-4799-8009-3 publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '6678' relation: later_version status: public status: public title: How to achieve the capacity of asymmetric channels type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '6739' abstract: - lang: eng text: 'We explore the relationship between polar and RM codes and we describe a coding scheme which improves upon the performance of the standard polar code at practical block lengths. Our starting point is the experimental observation that RM codes have a smaller error probability than polar codes under MAP decoding. This motivates us to introduce a family of codes that “interpolates” between RM and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1 is the original polar code, and C α|α=0 is an RM code. Based on numerical observations, we remark that the error probability under MAP decoding is an increasing function of α. MAP decoding has in general exponential complexity, but empirically the performance of polar codes at finite block lengths is boosted by moving along the family Cinter even under low-complexity decoding schemes such as, for instance, belief propagation or successive cancellation list decoder. We demonstrate the performance gain via numerical simulations for transmission over the erasure channel as well as the Gaussian channel.' author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke citation: ama: 'Mondelli M, Hassani H, Urbanke R. From polar to Reed-Muller codes: A technique to improve the finite-length performance. IEEE Transactions on Communications. 2014;62(9):3084-3091. doi:10.1109/tcomm.2014.2345069' apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2014). From polar to Reed-Muller codes: A technique to improve the finite-length performance. IEEE Transactions on Communications. IEEE. https://doi.org/10.1109/tcomm.2014.2345069' chicago: 'Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” IEEE Transactions on Communications. IEEE, 2014. https://doi.org/10.1109/tcomm.2014.2345069.' ieee: 'M. Mondelli, H. Hassani, and R. Urbanke, “From polar to Reed-Muller codes: A technique to improve the finite-length performance,” IEEE Transactions on Communications, vol. 62, no. 9. IEEE, pp. 3084–3091, 2014.' ista: 'Mondelli M, Hassani H, Urbanke R. 2014. From polar to Reed-Muller codes: A technique to improve the finite-length performance. IEEE Transactions on Communications. 62(9), 3084–3091.' mla: 'Mondelli, Marco, et al. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” IEEE Transactions on Communications, vol. 62, no. 9, IEEE, 2014, pp. 3084–91, doi:10.1109/tcomm.2014.2345069.' short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Communications 62 (2014) 3084–3091. date_created: 2019-07-31T07:20:21Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T08:08:46Z day: '01' doi: 10.1109/tcomm.2014.2345069 extern: '1' external_id: arxiv: - '1401.3127' intvolume: ' 62' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1401.3127 month: '09' oa: 1 oa_version: Preprint page: 3084-3091 publication: IEEE Transactions on Communications publication_identifier: issn: - 0090-6778 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: 'From polar to Reed-Muller codes: A technique to improve the finite-length performance' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2014' ... --- _id: '6744' abstract: - lang: eng text: With the aim of extending the coverage and improving the performance of impulse radio ultra-wideband (UWB) systems, this paper focuses on developing a novel single differential encoded decode and forward (DF) non-cooperative relaying scheme (NCR). To favor simple receiver structures, differential noncoherent detection is employed which enables effective energy capture without any channel estimation. Putting emphasis on the general case of multi-hop relaying, we illustrate an original algorithm for the joint power allocation and path selection (JPAPS), minimizing an approximate expression of the overall bit error rate (BER). In particular, after deriving a closed-form power allocation strategy, the optimal path selection is reduced to a shortest path problem on a connected graph, which can be solved without any topology information with complexity O(N 3 ), N being the number of available relays of the network. An approximate scheme is also presented, which reduces the complexity to O(N 2 ) while showing a negligible performance loss, and for benchmarking purposes, an exhaustive-search based multi-hop DF cooperative strategy is derived. Simulation results for various network setups corroborate the effectiveness of the proposed low-complexity JPAPS algorithm, which favorably compares to existing AF and DF relaying methods. author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Qi full_name: Zhou, Qi last_name: Zhou - first_name: Vincenzo full_name: Lottici, Vincenzo last_name: Lottici - first_name: Xiaoli full_name: Ma, Xiaoli last_name: Ma citation: ama: Mondelli M, Zhou Q, Lottici V, Ma X. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. IEEE Transactions on Wireless Communications. 2014;13(3):1397-1409. doi:10.1109/twc.2014.020914.130669 apa: Mondelli, M., Zhou, Q., Lottici, V., & Ma, X. (2014). Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. IEEE Transactions on Wireless Communications. IEEE. https://doi.org/10.1109/twc.2014.020914.130669 chicago: Mondelli, Marco, Qi Zhou, Vincenzo Lottici, and Xiaoli Ma. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” IEEE Transactions on Wireless Communications. IEEE, 2014. https://doi.org/10.1109/twc.2014.020914.130669. ieee: M. Mondelli, Q. Zhou, V. Lottici, and X. Ma, “Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications,” IEEE Transactions on Wireless Communications, vol. 13, no. 3. IEEE, pp. 1397–1409, 2014. ista: Mondelli M, Zhou Q, Lottici V, Ma X. 2014. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. IEEE Transactions on Wireless Communications. 13(3), 1397–1409. mla: Mondelli, Marco, et al. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” IEEE Transactions on Wireless Communications, vol. 13, no. 3, IEEE, 2014, pp. 1397–409, doi:10.1109/twc.2014.020914.130669. short: M. Mondelli, Q. Zhou, V. Lottici, X. Ma, IEEE Transactions on Wireless Communications 13 (2014) 1397–1409. date_created: 2019-07-31T09:05:07Z date_published: 2014-03-20T00:00:00Z date_updated: 2021-01-12T08:08:48Z day: '20' doi: 10.1109/twc.2014.020914.130669 extern: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '03' oa_version: None page: 1397-1409 publication: IEEE Transactions on Wireless Communications publication_status: published publisher: IEEE quality_controlled: '1' status: public title: Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2014' ... --- _id: '10885' abstract: - lang: eng text: "Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.\r\nIn this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.\r\nWe present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games." acknowledgement: " Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award." alternative_title: - LNCS 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: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Emmanuel full_name: Filiot, Emmanuel last_name: Filiot - first_name: Jean-François full_name: Raskin, Jean-François last_name: Raskin citation: ama: 'Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular games. In: VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:78-97. doi:10.1007/978-3-642-54013-4_5' apa: 'Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J.-F. (2014). Doomsday equilibria for omega-regular games. In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 78–97). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_5' chicago: 'Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François Raskin. “Doomsday Equilibria for Omega-Regular Games.” In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, 8318:78–97. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_5.' ieee: 'K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria for omega-regular games,” in VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 78–97.' ista: 'Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 78–97.' mla: 'Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 78–97, doi:10.1007/978-3-642-54013-4_5.' short: 'K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.' conference: end_date: 2014-01-21 location: San Diego, CA, United States name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation' start_date: 2014-01-19 date_created: 2022-03-18T13:03:15Z date_published: 2014-01-30T00:00:00Z date_updated: 2023-02-23T12:52:24Z day: '30' department: - _id: KrCh doi: 10.1007/978-3-642-54013-4_5 ec_funded: 1 external_id: arxiv: - '1311.3238' intvolume: ' 8318' language: - iso: eng month: '01' oa_version: Preprint page: 78-97 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' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 'VMCAI 2014: Verification, Model Checking, and Abstract Interpretation' publication_identifier: eisbn: - '9783642540134' eissn: - 1611-3349 isbn: - '9783642540127' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '681' relation: later_version status: public scopus_import: '1' status: public title: Doomsday equilibria for omega-regular games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8318 year: '2014' ... --- _id: '6853' abstract: - lang: eng text: This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields. alternative_title: - SpringerBriefs in Applied Sciences and Technology article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Edelsbrunner H. A Short Course in Computational Geometry and Topology. 1st ed. Cham: Springer Nature; 2014. doi:10.1007/978-3-319-05957-0' apa: 'Edelsbrunner, H. (2014). A Short Course in Computational Geometry and Topology (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-05957-0' chicago: 'Edelsbrunner, Herbert. A Short Course in Computational Geometry and Topology. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-05957-0.' ieee: 'H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed. Cham: Springer Nature, 2014.' ista: 'Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p.' mla: Edelsbrunner, Herbert. A Short Course in Computational Geometry and Topology. 1st ed., Springer Nature, 2014, doi:10.1007/978-3-319-05957-0. short: H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014. date_created: 2019-09-06T09:22:33Z date_published: 2014-01-01T00:00:00Z date_updated: 2022-03-04T07:47:54Z day: '01' department: - _id: HeEd doi: 10.1007/978-3-319-05957-0 edition: '1' language: - iso: eng month: '01' oa_version: None page: IX, 110 place: Cham publication_identifier: eisbn: - 9-783-3190-5957-0 eissn: - 2191-5318 isbn: - 9-783-3190-5956-3 issn: - 2191-530X publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: available as eBook via catalog IST BookList relation: other url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106 - description: available via catalog IST BookList relation: other url: https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842 scopus_import: '1' series_title: SpringerBriefs in Applied Sciences and Technology status: public title: A Short Course in Computational Geometry and Topology type: book user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '7038' article_processing_charge: No author: - first_name: Kristóf full_name: Huszár, Kristóf id: 33C26278-F248-11E8-B48F-1D18A9856A87 last_name: Huszár orcid: 0000-0002-5445-5057 - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Huszár K, Rolinek M. Playful Math - An Introduction to Mathematical Games. IST Austria apa: Huszár, K., & Rolinek, M. (n.d.). Playful Math - An introduction to mathematical games. IST Austria. chicago: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction to Mathematical Games. IST Austria, n.d. ieee: K. Huszár and M. Rolinek, Playful Math - An introduction to mathematical games. IST Austria. ista: Huszár K, Rolinek M. Playful Math - An introduction to mathematical games, IST Austria, 5p. mla: Huszár, Kristóf, and Michal Rolinek. Playful Math - An Introduction to Mathematical Games. IST Austria. short: K. Huszár, M. Rolinek, Playful Math - An Introduction to Mathematical Games, IST Austria, n.d. date_created: 2019-11-18T15:57:05Z date_published: 2014-06-30T00:00:00Z date_updated: 2020-07-14T23:11:45Z day: '30' ddc: - '510' department: - _id: VlKo - _id: UlWa file: - access_level: open_access checksum: 2b94e5e1f4c3fe8ab89b12806276fb09 content_type: application/pdf creator: dernst date_created: 2019-11-18T15:57:51Z date_updated: 2020-07-14T12:47:48Z file_id: '7039' file_name: 2014_Playful_Math_Huszar.pdf file_size: 511233 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '5' publication_status: draft publisher: IST Austria status: public title: Playful Math - An introduction to mathematical games type: working_paper user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '7071' abstract: - lang: eng text: Spin and orbital quantum numbers play a key role in the physics of Mott insulators, but in most systems they are connected only indirectly—via the Pauli exclusion principle and the Coulomb interaction. Iridium-based oxides (iridates) introduce strong spin–orbit coupling directly, such that these numbers become entwined together and the Mott physics attains a strong orbital character. In the layered honeycomb iridates this is thought to generate highly spin–anisotropic magnetic interactions, coupling the spin to a given spatial direction of exchange and leading to strongly frustrated magnetism. Here we report a new iridate structure that has the same local connectivity as the layered honeycomb and exhibits striking evidence for highly spin–anisotropic exchange. The basic structural units of this material suggest that a new family of three-dimensional structures could exist, the ‘harmonic honeycomb’ iridates, of which the present compound is the first example. article_number: '4203' article_processing_charge: No article_type: original author: - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Tess E. full_name: Smidt, Tess E. last_name: Smidt - first_name: Itamar full_name: Kimchi, Itamar last_name: Kimchi - first_name: Nicholas P. full_name: Breznay, Nicholas P. last_name: Breznay - first_name: Alun full_name: Biffin, Alun last_name: Biffin - first_name: Sungkyun full_name: Choi, Sungkyun last_name: Choi - first_name: Roger D. full_name: Johnson, Roger D. last_name: Johnson - first_name: Radu full_name: Coldea, Radu last_name: Coldea - first_name: Pilanda full_name: Watkins-Curry, Pilanda last_name: Watkins-Curry - first_name: Gregory T. full_name: McCandless, Gregory T. last_name: McCandless - first_name: Julia Y. full_name: Chan, Julia Y. last_name: Chan - first_name: Felipe full_name: Gandara, Felipe last_name: Gandara - first_name: Z. full_name: Islam, Z. last_name: Islam - first_name: Ashvin full_name: Vishwanath, Ashvin last_name: Vishwanath - first_name: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: Ross D. full_name: McDonald, Ross D. last_name: McDonald - first_name: James G. full_name: Analytis, James G. last_name: Analytis citation: ama: Modic KA, Smidt TE, Kimchi I, et al. Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate. Nature Communications. 2014;5. doi:10.1038/ncomms5203 apa: Modic, K. A., Smidt, T. E., Kimchi, I., Breznay, N. P., Biffin, A., Choi, S., … Analytis, J. G. (2014). Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate. Nature Communications. Springer Science and Business Media LLC. https://doi.org/10.1038/ncomms5203 chicago: Modic, Kimberly A, Tess E. Smidt, Itamar Kimchi, Nicholas P. Breznay, Alun Biffin, Sungkyun Choi, Roger D. Johnson, et al. “Realization of a Three-Dimensional Spin–Anisotropic Harmonic Honeycomb Iridate.” Nature Communications. Springer Science and Business Media LLC, 2014. https://doi.org/10.1038/ncomms5203. ieee: K. A. Modic et al., “Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate,” Nature Communications, vol. 5. Springer Science and Business Media LLC, 2014. ista: Modic KA, Smidt TE, Kimchi I, Breznay NP, Biffin A, Choi S, Johnson RD, Coldea R, Watkins-Curry P, McCandless GT, Chan JY, Gandara F, Islam Z, Vishwanath A, Shekhter A, McDonald RD, Analytis JG. 2014. Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate. Nature Communications. 5, 4203. mla: Modic, Kimberly A., et al. “Realization of a Three-Dimensional Spin–Anisotropic Harmonic Honeycomb Iridate.” Nature Communications, vol. 5, 4203, Springer Science and Business Media LLC, 2014, doi:10.1038/ncomms5203. short: K.A. Modic, T.E. Smidt, I. Kimchi, N.P. Breznay, A. Biffin, S. Choi, R.D. Johnson, R. Coldea, P. Watkins-Curry, G.T. McCandless, J.Y. Chan, F. Gandara, Z. Islam, A. Vishwanath, A. Shekhter, R.D. McDonald, J.G. Analytis, Nature Communications 5 (2014). date_created: 2019-11-19T13:22:39Z date_published: 2014-06-27T00:00:00Z date_updated: 2021-01-12T08:11:42Z day: '27' ddc: - '530' doi: 10.1038/ncomms5203 extern: '1' file: - access_level: open_access checksum: d290f0bfa93c5169cc6c8086874c5a78 content_type: application/pdf creator: dernst date_created: 2019-11-26T12:44:23Z date_updated: 2020-07-14T12:47:48Z file_id: '7113' file_name: 2014_NatureComm_Modic.pdf file_size: 4832820 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Science and Business Media LLC quality_controlled: '1' status: public title: Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate 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: '2014' ... --- _id: '7072' abstract: - lang: eng text: We investigate the structural and magnetic properties of two molecule-based magnets synthesized from the same starting components. Their different structural motifs promote contrasting exchange pathways and consequently lead to markedly different magnetic ground states. Through examination of their structural and magnetic properties we show that [Cu(pyz)(H2O)(gly)2](ClO4)2 may be considered a quasi-one-dimensional quantum Heisenberg antiferromagnet whereas the related compound [Cu(pyz)(gly)](ClO4), which is formed from dimers of antiferromagnetically interacting Cu2+ spins, remains disordered down to at least 0.03 K in zero field but shows a field-temperature phase diagram reminiscent of that seen in materials showing a Bose-Einstein condensation of magnons. article_number: '207201' article_processing_charge: No article_type: original author: - first_name: T. full_name: Lancaster, T. last_name: Lancaster - first_name: P. A. full_name: Goddard, P. A. last_name: Goddard - first_name: S. J. full_name: Blundell, S. J. last_name: Blundell - first_name: F. R. full_name: Foronda, F. R. last_name: Foronda - first_name: S. full_name: Ghannadzadeh, S. last_name: Ghannadzadeh - first_name: J. S. full_name: Möller, J. S. last_name: Möller - first_name: P. J. full_name: Baker, P. J. last_name: Baker - first_name: F. L. full_name: Pratt, F. L. last_name: Pratt - first_name: C. full_name: Baines, C. last_name: Baines - first_name: L. full_name: Huang, L. last_name: Huang - first_name: J. full_name: Wosnitza, J. last_name: Wosnitza - first_name: R. D. full_name: McDonald, R. D. last_name: McDonald - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: J. full_name: Singleton, J. last_name: Singleton - first_name: C. V. full_name: Topping, C. V. last_name: Topping - first_name: T. A. W. full_name: Beale, T. A. W. last_name: Beale - first_name: F. full_name: Xiao, F. last_name: Xiao - first_name: J. A. full_name: Schlueter, J. A. last_name: Schlueter - first_name: A. M. full_name: Barton, A. M. last_name: Barton - first_name: R. D. full_name: Cabrera, R. D. last_name: Cabrera - first_name: K. E. full_name: Carreiro, K. E. last_name: Carreiro - first_name: H. E. full_name: Tran, H. E. last_name: Tran - first_name: J. L. full_name: Manson, J. L. last_name: Manson citation: ama: Lancaster T, Goddard PA, Blundell SJ, et al. Controlling magnetic order and quantum disorder in molecule-based magnets. Physical Review Letters. 2014;112(20). doi:10.1103/physrevlett.112.207201 apa: Lancaster, T., Goddard, P. A., Blundell, S. J., Foronda, F. R., Ghannadzadeh, S., Möller, J. S., … Manson, J. L. (2014). Controlling magnetic order and quantum disorder in molecule-based magnets. Physical Review Letters. APS. https://doi.org/10.1103/physrevlett.112.207201 chicago: Lancaster, T., P. A. Goddard, S. J. Blundell, F. R. Foronda, S. Ghannadzadeh, J. S. Möller, P. J. Baker, et al. “Controlling Magnetic Order and Quantum Disorder in Molecule-Based Magnets.” Physical Review Letters. APS, 2014. https://doi.org/10.1103/physrevlett.112.207201. ieee: T. Lancaster et al., “Controlling magnetic order and quantum disorder in molecule-based magnets,” Physical Review Letters, vol. 112, no. 20. APS, 2014. ista: Lancaster T, Goddard PA, Blundell SJ, Foronda FR, Ghannadzadeh S, Möller JS, Baker PJ, Pratt FL, Baines C, Huang L, Wosnitza J, McDonald RD, Modic KA, Singleton J, Topping CV, Beale TAW, Xiao F, Schlueter JA, Barton AM, Cabrera RD, Carreiro KE, Tran HE, Manson JL. 2014. Controlling magnetic order and quantum disorder in molecule-based magnets. Physical Review Letters. 112(20), 207201. mla: Lancaster, T., et al. “Controlling Magnetic Order and Quantum Disorder in Molecule-Based Magnets.” Physical Review Letters, vol. 112, no. 20, 207201, APS, 2014, doi:10.1103/physrevlett.112.207201. short: T. Lancaster, P.A. Goddard, S.J. Blundell, F.R. Foronda, S. Ghannadzadeh, J.S. Möller, P.J. Baker, F.L. Pratt, C. Baines, L. Huang, J. Wosnitza, R.D. McDonald, K.A. Modic, J. Singleton, C.V. Topping, T.A.W. Beale, F. Xiao, J.A. Schlueter, A.M. Barton, R.D. Cabrera, K.E. Carreiro, H.E. Tran, J.L. Manson, Physical Review Letters 112 (2014). date_created: 2019-11-19T13:23:13Z date_published: 2014-05-19T00:00:00Z date_updated: 2021-01-12T08:11:42Z day: '19' doi: 10.1103/physrevlett.112.207201 extern: '1' intvolume: ' 112' issue: '20' language: - iso: eng month: '05' oa_version: None publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: APS quality_controlled: '1' status: public title: Controlling magnetic order and quantum disorder in molecule-based magnets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2014' ... --- _id: '7303' abstract: - lang: eng text: The electrolyte in the non-aqueous (aprotic) lithium air battery has a profound influence on the reactions that occur at the anode and cathode, and hence its overall operation on discharge/charge. It must possess a wide range of attributes, exceeding the requirements of electrolytes for Lithium ion batteries by far. The most important additional issues are stability at both anode and cathode in the presence of O2. The known problems with cycling the Li metal/non-aqueous electrolyte interface are further complicated by O2. New and much less understood are the reactions at the O2 cathode/electrolyte interface where the highly reversible formation/decomposition of Li2O2 on discharge/charge is critical for the operation of the non-aqueous lithium air battery. Many aprotic electrolytes exhibit decomposition at the cathode during discharge and charge due to the presence of reactive reduced O2 species affecting potential, capacity and kinetics on discharge and charge, cyclability and calendar life. Identifying suitable electrolytes is one of the key challenges for the non-aqueous lithium air battery at the present time. Following the realisation that cyclability of such cells in the initially used organic carbonate electrolytes is due to back-to-back irreversible reactions the stability of the non-aqueous electrolytes became a major focus of research on rechargeable lithium air batteries. This realisation led to the establishment of a suite of experimental and computational methods capable of screening the stability of electrolytes. These allow for greater mechanistic understanding of the reactivity and guide the way towards designing more stable systems. A range of electrolytes based on ethers, amides, sulfones, ionic liquids and dimethyl sulfoxide have been investigated. All are more stable than the organic carbonates, but not all are equally stable. Even though it was soon realised, by a number of groups, that ethers exhibit side reactions on discharge and charge, they still remain the choice in many studies. To date dimethyl sulfoxide and dimethylacetamide were identified as the most stable electrolytes. In conjunction with the investigation of electrolyte stability the importance of electrode stability became more prominent. The stability of the electrolyte cannot be considered in isolation. Its stability depends on the synergy between electrolyte and electrode. Carbon based electrodes promote electrolyte decomposition and decompose on their own. Although great progress has been made in only a few years, future work on aprotic electrolytes for Li-O2 batteries will need to explore other electrolytes in the quest for yet lower cost, higher safety, stability and low volatility. article_processing_charge: No author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Fanny full_name: Bardé, Fanny last_name: Bardé - first_name: Kensuke full_name: Takechi, Kensuke last_name: Takechi - first_name: Fuminori full_name: Mizuno, Fuminori last_name: Mizuno - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: 'Freunberger SA, Chen Y, Bardé F, Takechi K, Mizuno F, Bruce PG. Nonaqueous Electrolytes. In: Imanishi N, Luntz AC, Bruce P, eds. The Lithium Air Battery: Fundamentals. New York, NY: Springer Nature; 2014:23-58. doi:10.1007/978-1-4899-8062-5_2' apa: 'Freunberger, S. A., Chen, Y., Bardé, F., Takechi, K., Mizuno, F., & Bruce, P. G. (2014). Nonaqueous Electrolytes. In N. Imanishi, A. C. Luntz, & P. Bruce (Eds.), The Lithium Air Battery: Fundamentals (pp. 23–58). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-4899-8062-5_2' chicago: 'Freunberger, Stefan Alexander, Yuhui Chen, Fanny Bardé, Kensuke Takechi, Fuminori Mizuno, and Peter G. Bruce. “Nonaqueous Electrolytes.” In The Lithium Air Battery: Fundamentals, edited by Nobuyuki Imanishi, Alan C. Luntz, and Peter Bruce, 23–58. New York, NY: Springer Nature, 2014. https://doi.org/10.1007/978-1-4899-8062-5_2.' ieee: 'S. A. Freunberger, Y. Chen, F. Bardé, K. Takechi, F. Mizuno, and P. G. Bruce, “Nonaqueous Electrolytes,” in The Lithium Air Battery: Fundamentals, N. Imanishi, A. C. Luntz, and P. Bruce, Eds. New York, NY: Springer Nature, 2014, pp. 23–58.' ista: 'Freunberger SA, Chen Y, Bardé F, Takechi K, Mizuno F, Bruce PG. 2014.Nonaqueous Electrolytes. In: The Lithium Air Battery: Fundamentals. , 23–58.' mla: 'Freunberger, Stefan Alexander, et al. “Nonaqueous Electrolytes.” The Lithium Air Battery: Fundamentals, edited by Nobuyuki Imanishi et al., Springer Nature, 2014, pp. 23–58, doi:10.1007/978-1-4899-8062-5_2.' short: 'S.A. Freunberger, Y. Chen, F. Bardé, K. Takechi, F. Mizuno, P.G. Bruce, in:, N. Imanishi, A.C. Luntz, P. Bruce (Eds.), The Lithium Air Battery: Fundamentals, Springer Nature, New York, NY, 2014, pp. 23–58.' date_created: 2020-01-15T12:17:55Z date_published: 2014-03-05T00:00:00Z date_updated: 2021-01-12T08:12:54Z day: '05' doi: 10.1007/978-1-4899-8062-5_2 editor: - first_name: Nobuyuki full_name: Imanishi, Nobuyuki last_name: Imanishi - first_name: Alan C. full_name: Luntz, Alan C. last_name: Luntz - first_name: Peter full_name: Bruce, Peter last_name: Bruce extern: '1' language: - iso: eng month: '03' oa_version: None page: 23-58 place: New York, NY publication: 'The Lithium Air Battery: Fundamentals' publication_identifier: eisbn: - '9781489980625' isbn: - '9781489980618' publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Nonaqueous Electrolytes type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '7302' abstract: - lang: eng text: Understanding charge carrier transport in Li2O2, the storage material in the non-aqueous Li-O2 battery, is key to the development of this high-energy battery. Here, we studied ionic transport properties and Li self-diffusion in nanocrystalline Li2O2 by conductivity and temperature variable 7Li NMR spectroscopy. Nanostructured Li2O2, characterized by a mean crystallite size of less than 50 nm as estimated from X-ray diffraction peak broadening, was prepared by high-energy ball milling of microcrystalline lithium peroxide with μm sized crystallites. At room temperature the overall conductivity σ of the microcrystalline reference sample turned out to be very low (3.4 × 10−13 S cm−1) which is in agreement with results from temperature-variable 7Li NMR line shape measurements. Ball-milling, however, leads to an increase of σ by approximately two orders of magnitude (1.1 × 10−10 S cm−1); correspondingly, the activation energy decreases from 0.89 eV to 0.82 eV. The electronic contribution σeon, however, is in the order of 9 × 10−12 S cm−1 which makes less than 10% of the total value. Interestingly, 7Li NMR lines of nano-Li2O2 undergo pronounced heterogeneous motional narrowing which manifests in a two-component line shape emerging with increasing temperatures. Most likely, the enhancement in σ can be traced back to the generation of a spin reservoir with highly mobile Li ions; these are expected to reside in the nearest neighbourhood of defects generated or near the structurally disordered and defect-rich interfacial regions formed during mechanical treatment. article_processing_charge: No article_type: original author: - first_name: A. full_name: Dunst, A. last_name: Dunst - first_name: V. full_name: Epp, V. last_name: Epp - first_name: I. full_name: Hanzu, I. last_name: Hanzu - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: M. full_name: Wilkening, M. last_name: Wilkening citation: ama: Dunst A, Epp V, Hanzu I, Freunberger SA, Wilkening M. Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries. Energy & Environmental Science. 2014;7(8):2739-2752. doi:10.1039/c4ee00496e apa: Dunst, A., Epp, V., Hanzu, I., Freunberger, S. A., & Wilkening, M. (2014). Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries. Energy & Environmental Science. RSC. https://doi.org/10.1039/c4ee00496e chicago: Dunst, A., V. Epp, I. Hanzu, Stefan Alexander Freunberger, and M. Wilkening. “Short-Range Li Diffusion vs. Long-Range Ionic Conduction in Nanocrystalline Lithium Peroxide Li2O2—the Discharge Product in Lithium-Air Batteries.” Energy & Environmental Science. RSC, 2014. https://doi.org/10.1039/c4ee00496e. ieee: A. Dunst, V. Epp, I. Hanzu, S. A. Freunberger, and M. Wilkening, “Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries,” Energy & Environmental Science, vol. 7, no. 8. RSC, pp. 2739–2752, 2014. ista: Dunst A, Epp V, Hanzu I, Freunberger SA, Wilkening M. 2014. Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries. Energy & Environmental Science. 7(8), 2739–2752. mla: Dunst, A., et al. “Short-Range Li Diffusion vs. Long-Range Ionic Conduction in Nanocrystalline Lithium Peroxide Li2O2—the Discharge Product in Lithium-Air Batteries.” Energy & Environmental Science, vol. 7, no. 8, RSC, 2014, pp. 2739–52, doi:10.1039/c4ee00496e. short: A. Dunst, V. Epp, I. Hanzu, S.A. Freunberger, M. Wilkening, Energy & Environmental Science 7 (2014) 2739–2752. date_created: 2020-01-15T12:17:43Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:12:53Z day: '01' doi: 10.1039/c4ee00496e extern: '1' intvolume: ' 7' issue: '8' language: - iso: eng month: '08' oa_version: Published Version page: 2739-2752 publication: Energy & Environmental Science publication_identifier: issn: - 1754-5692 - 1754-5706 publication_status: published publisher: RSC quality_controlled: '1' status: public title: Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2014' ... --- _id: '7305' abstract: - lang: eng text: When lithium–oxygen batteries discharge, O2 is reduced at the cathode to form solid Li2O2. Understanding the fundamental mechanism of O2 reduction in aprotic solvents is therefore essential to realizing their technological potential. Two different models have been proposed for Li2O2 formation, involving either solution or electrode surface routes. Here, we describe a single unified mechanism, which, unlike previous models, can explain O2 reduction across the whole range of solvents and for which the two previous models are limiting cases. We observe that the solvent influences O2 reduction through its effect on the solubility of LiO2, or, more precisely, the free energy of the reaction LiO2* ⇌ Li(sol)+ + O2−(sol) + ion pairs + higher aggregates (clusters). The unified mechanism shows that low-donor-number solvents are likely to lead to premature cell death, and that the future direction of research for lithium–oxygen batteries should focus on the search for new, stable, high-donor-number electrolytes, because they can support higher capacities and can better sustain discharge. article_processing_charge: No article_type: original author: - first_name: Lee full_name: Johnson, Lee last_name: Johnson - first_name: Chunmei full_name: Li, Chunmei last_name: Li - first_name: Zheng full_name: Liu, Zheng last_name: Liu - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Praveen C. full_name: Ashok, Praveen C. last_name: Ashok - first_name: Bavishna B. full_name: Praveen, Bavishna B. last_name: Praveen - first_name: Kishan full_name: Dholakia, Kishan last_name: Dholakia - first_name: Jean-Marie full_name: Tarascon, Jean-Marie last_name: Tarascon - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Johnson L, Li C, Liu Z, et al. The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry. 2014;6(12):1091-1099. doi:10.1038/nchem.2101 apa: Johnson, L., Li, C., Liu, Z., Chen, Y., Freunberger, S. A., Ashok, P. C., … Bruce, P. G. (2014). The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2101 chicago: Johnson, Lee, Chunmei Li, Zheng Liu, Yuhui Chen, Stefan Alexander Freunberger, Praveen C. Ashok, Bavishna B. Praveen, Kishan Dholakia, Jean-Marie Tarascon, and Peter G. Bruce. “The Role of LiO2 Solubility in O2 Reduction in Aprotic Solvents and Its Consequences for Li–O2 Batteries.” Nature Chemistry. Springer Nature, 2014. https://doi.org/10.1038/nchem.2101. ieee: L. Johnson et al., “The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries,” Nature Chemistry, vol. 6, no. 12. Springer Nature, pp. 1091–1099, 2014. ista: Johnson L, Li C, Liu Z, Chen Y, Freunberger SA, Ashok PC, Praveen BB, Dholakia K, Tarascon J-M, Bruce PG. 2014. The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry. 6(12), 1091–1099. mla: Johnson, Lee, et al. “The Role of LiO2 Solubility in O2 Reduction in Aprotic Solvents and Its Consequences for Li–O2 Batteries.” Nature Chemistry, vol. 6, no. 12, Springer Nature, 2014, pp. 1091–99, doi:10.1038/nchem.2101. short: L. Johnson, C. Li, Z. Liu, Y. Chen, S.A. Freunberger, P.C. Ashok, B.B. Praveen, K. Dholakia, J.-M. Tarascon, P.G. Bruce, Nature Chemistry 6 (2014) 1091–1099. date_created: 2020-01-15T12:18:18Z date_published: 2014-11-10T00:00:00Z date_updated: 2021-01-12T08:12:55Z day: '10' doi: 10.1038/nchem.2101 extern: '1' intvolume: ' 6' issue: '12' language: - iso: eng month: '11' oa_version: None page: 1091-1099 publication: Nature Chemistry publication_identifier: issn: - 1755-4330 - 1755-4349 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/nchem.2138 status: public title: The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2014' ... --- _id: '7304' abstract: - lang: eng text: Lithium-air batteries have received extraordinary attention recently owing to their theoretical gravimetric energies being considerably higher than those of Li-ion batteries. There are, however, significant challenges to practical implementation, including low energy efficiency, cycle life, and power capability. These are due primarily to the lack of fundamental understanding of oxygen reduction and evolution reaction kinetics and parasitic reactions between oxygen redox intermediate species and nominally inactive battery components such as carbon in the oxygen electrode and electrolytes. In this article, we discuss recent advances in the mechanistic understanding of oxygen redox reactions in nonaqueous electrolytes and the search for electrolytes and electrode materials that are chemically stable in the oxygen electrode. In addition, methods to protect lithium metal against corrosion by water and dendrite formation in aqueous lithium-air batteries are discussed. Further materials innovations lie at the heart of research and development efforts that are needed to enable the development of lithium-oxygen batteries with enhanced round-trip efficiency and cycle life. article_processing_charge: No article_type: original author: - first_name: D.G. full_name: Kwabi, D.G. last_name: Kwabi - first_name: N. full_name: Ortiz-Vitoriano, N. last_name: Ortiz-Vitoriano - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Y. full_name: Chen, Y. last_name: Chen - first_name: N. full_name: Imanishi, N. last_name: Imanishi - first_name: P.G. full_name: Bruce, P.G. last_name: Bruce - first_name: Y. full_name: Shao-Horn, Y. last_name: Shao-Horn citation: ama: Kwabi DG, Ortiz-Vitoriano N, Freunberger SA, et al. Materials challenges in rechargeable lithium-air batteries. MRS Bulletin. 2014;39(5):443-452. doi:10.1557/mrs.2014.87 apa: Kwabi, D. G., Ortiz-Vitoriano, N., Freunberger, S. A., Chen, Y., Imanishi, N., Bruce, P. G., & Shao-Horn, Y. (2014). Materials challenges in rechargeable lithium-air batteries. MRS Bulletin. CUP. https://doi.org/10.1557/mrs.2014.87 chicago: Kwabi, D.G., N. Ortiz-Vitoriano, Stefan Alexander Freunberger, Y. Chen, N. Imanishi, P.G. Bruce, and Y. Shao-Horn. “Materials Challenges in Rechargeable Lithium-Air Batteries.” MRS Bulletin. CUP, 2014. https://doi.org/10.1557/mrs.2014.87. ieee: D. G. Kwabi et al., “Materials challenges in rechargeable lithium-air batteries,” MRS Bulletin, vol. 39, no. 5. CUP, pp. 443–452, 2014. ista: Kwabi DG, Ortiz-Vitoriano N, Freunberger SA, Chen Y, Imanishi N, Bruce PG, Shao-Horn Y. 2014. Materials challenges in rechargeable lithium-air batteries. MRS Bulletin. 39(5), 443–452. mla: Kwabi, D. G., et al. “Materials Challenges in Rechargeable Lithium-Air Batteries.” MRS Bulletin, vol. 39, no. 5, CUP, 2014, pp. 443–52, doi:10.1557/mrs.2014.87. short: D.G. Kwabi, N. Ortiz-Vitoriano, S.A. Freunberger, Y. Chen, N. Imanishi, P.G. Bruce, Y. Shao-Horn, MRS Bulletin 39 (2014) 443–452. date_created: 2020-01-15T12:18:05Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T08:12:54Z day: '01' doi: 10.1557/mrs.2014.87 extern: '1' intvolume: ' 39' issue: '5' language: - iso: eng month: '05' oa_version: None page: 443-452 publication: MRS Bulletin publication_identifier: issn: - 0883-7694 - 1938-1425 publication_status: published publisher: CUP quality_controlled: '1' status: public title: Materials challenges in rechargeable lithium-air batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 39 year: '2014' ... --- _id: '7301' abstract: - lang: eng text: Several problems arise at the O2 (positive) electrode in the Li-air battery, including solvent/electrode decomposition and electrode passivation by insulating Li2O2. Progress partially depends on exploring the basic electrochemistry of O2 reduction. Here we describe the effect of complexing-cations on the electrochemical reduction of O2 in DMSO in the presence and absence of a Li salt. The solubility of alkaline peroxides in DMSO is enhanced by the complexing-cations, consistent with their strong interaction with reduced O2. The complexing-cations also increase the rate of the 1-electron O2 reduction to O2•– by up to six-fold (k° = 2.4 ×10–3 to 1.5 × 10–2 cm s–1) whether or not Li+ ions are present. In the absence of Li+, the complexing-cations also promote the reduction of O2•– to O22–. In the presence of Li+ and complexing-cations, and despite the interaction of the reduced O2 with the latter, SERS confirms that the product is still Li2O2. article_processing_charge: No article_type: original author: - first_name: Chunmei full_name: Li, Chunmei last_name: Li - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Lee full_name: Johnson, Lee last_name: Johnson - first_name: Sylvie full_name: Grugeon, Sylvie last_name: Grugeon - first_name: Stéphane full_name: Laruelle, Stéphane last_name: Laruelle - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce - first_name: Michel full_name: Armand, Michel last_name: Armand citation: ama: 'Li C, Fontaine O, Freunberger SA, et al. Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry C. 2014;118(7):3393-3401. doi:10.1021/jp4093805' apa: 'Li, C., Fontaine, O., Freunberger, S. A., Johnson, L., Grugeon, S., Laruelle, S., … Armand, M. (2014). Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry C. ACS. https://doi.org/10.1021/jp4093805' chicago: 'Li, Chunmei, Olivier Fontaine, Stefan Alexander Freunberger, Lee Johnson, Sylvie Grugeon, Stéphane Laruelle, Peter G. Bruce, and Michel Armand. “Aprotic Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic Solvent.” The Journal of Physical Chemistry C. ACS, 2014. https://doi.org/10.1021/jp4093805.' ieee: 'C. Li et al., “Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent,” The Journal of Physical Chemistry C, vol. 118, no. 7. ACS, pp. 3393–3401, 2014.' ista: 'Li C, Fontaine O, Freunberger SA, Johnson L, Grugeon S, Laruelle S, Bruce PG, Armand M. 2014. Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry C. 118(7), 3393–3401.' mla: 'Li, Chunmei, et al. “Aprotic Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic Solvent.” The Journal of Physical Chemistry C, vol. 118, no. 7, ACS, 2014, pp. 3393–401, doi:10.1021/jp4093805.' short: C. Li, O. Fontaine, S.A. Freunberger, L. Johnson, S. Grugeon, S. Laruelle, P.G. Bruce, M. Armand, The Journal of Physical Chemistry C 118 (2014) 3393–3401. date_created: 2020-01-15T12:17:28Z date_published: 2014-01-29T00:00:00Z date_updated: 2021-01-12T08:12:53Z day: '29' doi: 10.1021/jp4093805 extern: '1' intvolume: ' 118' issue: '7' language: - iso: eng month: '01' oa_version: None page: 3393-3401 publication: The Journal of Physical Chemistry C publication_identifier: issn: - 1932-7447 - 1932-7455 publication_status: published publisher: ACS quality_controlled: '1' status: public title: 'Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2014' ... --- _id: '7300' abstract: - lang: eng text: Photoinduced electron transfer (PET), which causes pH-dependent quenching of fluorescent dyes, is more effectively introduced by phenolic groups than by amino groups which have been much more commonly used so far. That is demonstrated by fluorescence measurements involving several classes of fluorophores. Electrochemical measurements show that PET in several amino-modified dyes is thermodynamically favorable, even though it was not experimentally found, underlining the importance of kinetic aspects to the process. Consequently, the attachment of phenolic groups allows for fast and simple preparation of a wide selection of fluorescent pH-probes with tailor-made spectral properties, sensitive ranges, and individual advantages, so that a large number of applications can be realized. Fluorophores carrying phenolic groups may also be used for sensing analytes other than pH or molecular switching and signaling. article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Aigner, Daniel last_name: Aigner - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Martin full_name: Wilkening, Martin last_name: Wilkening - first_name: Robert full_name: Saf, Robert last_name: Saf - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Ingo full_name: Klimant, Ingo last_name: Klimant citation: ama: Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. Analytical Chemistry. 2014;86(18):9293-9300. doi:10.1021/ac502513g apa: Aigner, D., Freunberger, S. A., Wilkening, M., Saf, R., Borisov, S. M., & Klimant, I. (2014). Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. Analytical Chemistry. ACS. https://doi.org/10.1021/ac502513g chicago: Aigner, Daniel, Stefan Alexander Freunberger, Martin Wilkening, Robert Saf, Sergey M. Borisov, and Ingo Klimant. “Enhancing Photoinduced Electron Transfer Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry. ACS, 2014. https://doi.org/10.1021/ac502513g. ieee: D. Aigner, S. A. Freunberger, M. Wilkening, R. Saf, S. M. Borisov, and I. Klimant, “Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols,” Analytical Chemistry, vol. 86, no. 18. ACS, pp. 9293–9300, 2014. ista: Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. 2014. Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. Analytical Chemistry. 86(18), 9293–9300. mla: Aigner, Daniel, et al. “Enhancing Photoinduced Electron Transfer Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry, vol. 86, no. 18, ACS, 2014, pp. 9293–300, doi:10.1021/ac502513g. short: D. Aigner, S.A. Freunberger, M. Wilkening, R. Saf, S.M. Borisov, I. Klimant, Analytical Chemistry 86 (2014) 9293–9300. date_created: 2020-01-15T12:17:17Z date_published: 2014-08-14T00:00:00Z date_updated: 2021-01-12T08:12:53Z day: '14' doi: 10.1021/ac502513g extern: '1' intvolume: ' 86' issue: '18' language: - iso: eng month: '08' oa_version: None page: 9293-9300 publication: Analytical Chemistry publication_identifier: issn: - 0003-2700 - 1520-6882 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2014' ... --- _id: '7361' abstract: - lang: eng text: Bistable switches are fundamental regulatory elements of complex systems, ranging from electronics to living cells. Designed genetic toggle switches have been constructed from pairs of natural transcriptional repressors wired to inhibit one another. The complexity of the engineered regulatory circuits can be increased using orthogonal transcriptional regulators based on designed DNA-binding domains. However, a mutual repressor-based toggle switch comprising DNA-binding domains of transcription-activator-like effectors (TALEs) did not support bistability in mammalian cells. Here, the challenge of engineering a bistable switch based on monomeric DNA-binding domains is solved via the introduction of a positive feedback loop composed of activators based on the same TALE domains as their opposing repressors and competition for the same DNA operator site. This design introduces nonlinearity and results in epigenetic bistability. This principle could be used to employ other monomeric DNA-binding domains such as CRISPR for applications ranging from reprogramming cells to building digital biological memory. article_number: '5007' article_processing_charge: No article_type: original author: - first_name: Tina full_name: Lebar, Tina last_name: Lebar - first_name: Urban full_name: Bezeljak, Urban id: 2A58201A-F248-11E8-B48F-1D18A9856A87 last_name: Bezeljak orcid: 0000-0003-1365-5631 - first_name: Anja full_name: Golob, Anja last_name: Golob - first_name: Miha full_name: Jerala, Miha last_name: Jerala - first_name: Lucija full_name: Kadunc, Lucija last_name: Kadunc - first_name: Boštjan full_name: Pirš, Boštjan last_name: Pirš - first_name: Martin full_name: Stražar, Martin last_name: Stražar - first_name: Dušan full_name: Vučko, Dušan last_name: Vučko - first_name: Uroš full_name: Zupančič, Uroš last_name: Zupančič - first_name: Mojca full_name: Benčina, Mojca last_name: Benčina - first_name: Vida full_name: Forstnerič, Vida last_name: Forstnerič - first_name: Rok full_name: Gaber, Rok last_name: Gaber - first_name: Jan full_name: Lonzarić, Jan last_name: Lonzarić - first_name: Andreja full_name: Majerle, Andreja last_name: Majerle - first_name: Alja full_name: Oblak, Alja last_name: Oblak - first_name: Anže full_name: Smole, Anže last_name: Smole - first_name: Roman full_name: Jerala, Roman last_name: Jerala citation: ama: Lebar T, Bezeljak U, Golob A, et al. A bistable genetic switch based on designable DNA-binding domains. Nature Communications. 2014;5(1). doi:10.1038/ncomms6007 apa: Lebar, T., Bezeljak, U., Golob, A., Jerala, M., Kadunc, L., Pirš, B., … Jerala, R. (2014). A bistable genetic switch based on designable DNA-binding domains. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms6007 chicago: Lebar, Tina, Urban Bezeljak, Anja Golob, Miha Jerala, Lucija Kadunc, Boštjan Pirš, Martin Stražar, et al. “A Bistable Genetic Switch Based on Designable DNA-Binding Domains.” Nature Communications. Springer Nature, 2014. https://doi.org/10.1038/ncomms6007. ieee: T. Lebar et al., “A bistable genetic switch based on designable DNA-binding domains,” Nature Communications, vol. 5, no. 1. Springer Nature, 2014. ista: Lebar T, Bezeljak U, Golob A, Jerala M, Kadunc L, Pirš B, Stražar M, Vučko D, Zupančič U, Benčina M, Forstnerič V, Gaber R, Lonzarić J, Majerle A, Oblak A, Smole A, Jerala R. 2014. A bistable genetic switch based on designable DNA-binding domains. Nature Communications. 5(1), 5007. mla: Lebar, Tina, et al. “A Bistable Genetic Switch Based on Designable DNA-Binding Domains.” Nature Communications, vol. 5, no. 1, 5007, Springer Nature, 2014, doi:10.1038/ncomms6007. short: T. Lebar, U. Bezeljak, A. Golob, M. Jerala, L. Kadunc, B. Pirš, M. Stražar, D. Vučko, U. Zupančič, M. Benčina, V. Forstnerič, R. Gaber, J. Lonzarić, A. Majerle, A. Oblak, A. Smole, R. Jerala, Nature Communications 5 (2014). date_created: 2020-01-25T15:57:17Z date_published: 2014-09-29T00:00:00Z date_updated: 2021-01-12T08:13:15Z day: '29' doi: 10.1038/ncomms6007 extern: '1' external_id: pmid: - '25264186' intvolume: ' 5' issue: '1' language: - iso: eng month: '09' oa_version: None pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: A bistable genetic switch based on designable DNA-binding domains type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2014' ... --- _id: '7455' abstract: - lang: eng text: 'The reaction between NiO and (0001)- and ([1\bar102])-oriented Al2O3 single crystals has been investigated on model experimental systems by using the ReflEXAFS technique. Depth-sensitive information is obtained by collecting data above and below the critical angle for total reflection. A systematic protocol for data analysis, based on the recently developed CARD code, was implemented, and a detailed description of the reactive systems was obtained. In particular, for ([1\bar102])-oriented Al2O3, the reaction with NiO is almost complete after heating for 6 h at 1273 K, and an almost uniform layer of spinel is found below a mixed (NiO + spinel) layer at the very upmost part of the sample. In the case of the (0001)-oriented Al2O3, for the same temperature and heating time, the reaction shows a lower advancement degree and a residual fraction of at least 30% NiO is detected in the ReflEXAFS spectra. ' article_processing_charge: No article_type: original author: - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Federico full_name: Benzi, Federico last_name: Benzi - first_name: Paolo full_name: Ghigna, Paolo last_name: Ghigna - first_name: Sonia full_name: Pin, Sonia last_name: Pin - first_name: Giorgio full_name: Spinolo, Giorgio last_name: Spinolo - first_name: Francesco full_name: d'Acapito, Francesco last_name: d'Acapito citation: ama: Costanzo T, Benzi F, Ghigna P, Pin S, Spinolo G, d’Acapito F. Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS). Journal of Synchrotron Radiation. 2014;21(2):395-400. doi:10.1107/s1600577513031299 apa: Costanzo, T., Benzi, F., Ghigna, P., Pin, S., Spinolo, G., & d’Acapito, F. (2014). Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS). Journal of Synchrotron Radiation. International Union of Crystallography. https://doi.org/10.1107/s1600577513031299 chicago: Costanzo, Tommaso, Federico Benzi, Paolo Ghigna, Sonia Pin, Giorgio Spinolo, and Francesco d’Acapito. “Studying the Surface Reaction between NiO and Al2O3viatotal Reflection EXAFS (ReflEXAFS).” Journal of Synchrotron Radiation. International Union of Crystallography, 2014. https://doi.org/10.1107/s1600577513031299. ieee: T. Costanzo, F. Benzi, P. Ghigna, S. Pin, G. Spinolo, and F. d’Acapito, “Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS),” Journal of Synchrotron Radiation, vol. 21, no. 2. International Union of Crystallography, pp. 395–400, 2014. ista: Costanzo T, Benzi F, Ghigna P, Pin S, Spinolo G, d’Acapito F. 2014. Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS). Journal of Synchrotron Radiation. 21(2), 395–400. mla: Costanzo, Tommaso, et al. “Studying the Surface Reaction between NiO and Al2O3viatotal Reflection EXAFS (ReflEXAFS).” Journal of Synchrotron Radiation, vol. 21, no. 2, International Union of Crystallography, 2014, pp. 395–400, doi:10.1107/s1600577513031299. short: T. Costanzo, F. Benzi, P. Ghigna, S. Pin, G. Spinolo, F. d’Acapito, Journal of Synchrotron Radiation 21 (2014) 395–400. date_created: 2020-02-05T14:14:48Z date_published: 2014-01-10T00:00:00Z date_updated: 2023-02-23T13:08:22Z day: '10' doi: 10.1107/s1600577513031299 extern: '1' intvolume: ' 21' issue: '2' language: - iso: eng month: '01' oa_version: None page: 395-400 publication: Journal of Synchrotron Radiation publication_identifier: issn: - 1600-5775 publication_status: published publisher: International Union of Crystallography quality_controlled: '1' status: public title: Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2014' ... --- _id: '7598' article_processing_charge: No article_type: original author: - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Hong-Wei full_name: Xue, Hong-Wei last_name: Xue citation: ama: Tan S, Xue H-W. Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. Cell Reports. 2014;9(5):1692-1702. doi:10.1016/j.celrep.2014.10.047 apa: Tan, S., & Xue, H.-W. (2014). Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2014.10.047 chicago: Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis by Phosphorylating and Promoting the Turnover of ACS5.” Cell Reports. Elsevier, 2014. https://doi.org/10.1016/j.celrep.2014.10.047. ieee: S. Tan and H.-W. Xue, “Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5,” Cell Reports, vol. 9, no. 5. Elsevier, pp. 1692–1702, 2014. ista: Tan S, Xue H-W. 2014. Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. Cell Reports. 9(5), 1692–1702. mla: Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis by Phosphorylating and Promoting the Turnover of ACS5.” Cell Reports, vol. 9, no. 5, Elsevier, 2014, pp. 1692–702, doi:10.1016/j.celrep.2014.10.047. short: S. Tan, H.-W. Xue, Cell Reports 9 (2014) 1692–1702. date_created: 2020-03-21T16:08:18Z date_published: 2014-12-11T00:00:00Z date_updated: 2021-01-12T08:14:24Z day: '11' ddc: - '580' doi: 10.1016/j.celrep.2014.10.047 extern: '1' file: - access_level: open_access checksum: 23c30de4ac98ce9879fc054121517626 content_type: application/pdf creator: dernst date_created: 2020-03-23T12:23:40Z date_updated: 2020-07-14T12:48:01Z file_id: '7613' file_name: 2014_CellPress_Tan.pdf file_size: 2755808 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 9' issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Published Version page: 1692-1702 publication: Cell Reports publication_identifier: issn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5 tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '768' abstract: - lang: eng text: 'Task allocation is a classic distributed problem in which a set of p potentially faulty processes must cooperate to perform a set of tasks. This paper considers a new dynamic version of the problem, in which tasks are injected adversarially during an asynchronous execution. We give the first asynchronous shared-memory algorithm for dynamic task allocation, and we prove that our solution is optimal within logarithmic factors. The main algorithmic idea is a randomized concurrent data structure called a dynamic to-do tree, which allows processes to pick new tasks to perform at random from the set of available tasks, and to insert tasks at random empty locations in the data structure. Our analysis shows that these properties avoid duplicating work unnecessarily. On the other hand, since the adversary controls the input as well the scheduling, it can induce executions where lots of processes contend for a few available tasks, which is inefficient. However, we prove that every algorithm has the same problem: given an arbitrary input, if OPT is the worst-case complexity of the optimal algorithm on that input, then the expected work complexity of our algorithm on the same input is O(OPT log3 m), where m is an upper bound on the number of tasks that are present in the system at any given time.' acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nMichael A. Bender - This research was supported in part by NSF grants CCF 1114809, CCF 1217708, IIS 1247726, and IIS 1251137.\r\nRati Gelashvili - This work was supported in part by NSF grants CCF-1217921, CCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nSeth Gilbert - Supported by Singapore AcRF-2 MOE2011-T2-2-042.\r\n" article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Michael full_name: Bender, Michael last_name: Bender - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert citation: ama: 'Alistarh D-A, Aspnes J, Bender M, Gelashvili R, Gilbert S. Dynamic task allocation in asynchronous shared memory. In: SIAM; 2014:416-435. doi:10.1137/1.9781611973402.31' apa: 'Alistarh, D.-A., Aspnes, J., Bender, M., Gelashvili, R., & Gilbert, S. (2014). Dynamic task allocation in asynchronous shared memory (pp. 416–435). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1137/1.9781611973402.31' chicago: Alistarh, Dan-Adrian, James Aspnes, Michael Bender, Rati Gelashvili, and Seth Gilbert. “Dynamic Task Allocation in Asynchronous Shared Memory,” 416–35. SIAM, 2014. https://doi.org/10.1137/1.9781611973402.31. ieee: 'D.-A. Alistarh, J. Aspnes, M. Bender, R. Gelashvili, and S. Gilbert, “Dynamic task allocation in asynchronous shared memory,” presented at the SODA: Symposium on Discrete Algorithms, 2014, pp. 416–435.' ista: 'Alistarh D-A, Aspnes J, Bender M, Gelashvili R, Gilbert S. 2014. Dynamic task allocation in asynchronous shared memory. SODA: Symposium on Discrete Algorithms, 416–435.' mla: Alistarh, Dan-Adrian, et al. Dynamic Task Allocation in Asynchronous Shared Memory. SIAM, 2014, pp. 416–35, doi:10.1137/1.9781611973402.31. short: D.-A. Alistarh, J. Aspnes, M. Bender, R. Gelashvili, S. Gilbert, in:, SIAM, 2014, pp. 416–435. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T11:48:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T13:13:52Z day: '01' doi: 10.1137/1.9781611973402.31 extern: '1' language: - iso: eng month: '01' oa_version: None page: 416 - 435 publication_status: published publisher: SIAM publist_id: '6886' status: public title: Dynamic task allocation in asynchronous shared memory type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '769' abstract: - lang: eng text: 'This article presents the first tight bounds on the time complexity of shared-memory renaming, a fundamental problem in distributed computing in which a set of processes need to pick distinct identifiers from a small namespace. We first prove an individual lower bound of ω(k) process steps for deterministic renaming into any namespace of size subexponential in k, where k is the number of participants. The bound is tight: it draws an exponential separation between deterministic and randomized solutions, and implies new tight bounds for deterministic concurrent fetch-and-increment counters, queues, and stacks. The proof is based on a new reduction from renaming to another fundamental problem in distributed computing: mutual exclusion. We complement this individual bound with a global lower bound of ω(klog(k/c)) on the total step complexity of renaming into a namespace of size ck, for any c = 1. This result applies to randomized algorithms against a strong adversary, and helps derive new global lower bounds for randomized approximate counter implementations, that are tight within logarithmic factors. On the algorithmic side, we give a protocol that transforms any sorting network into a randomized strong adaptive renaming algorithm, with expected cost equal to the depth of the sorting network. This gives a tight adaptive renaming algorithm with expected step complexity O(log k), where k is the contention in the current execution. This algorithm is the first to achieve sublinear time, and it is time-optimal as per our randomized lower bound. Finally, we use this renaming protocol to build monotone-consistent counters with logarithmic step complexity and linearizable fetch-and-increment registers with polylogarithmic cost.' acknowledgement: "The work of J. Aspnes was supported in part by NSF grant CCF-0916389. The work of S. Gilbert was\r\nsupported by Singapore AcRF-2 MOE 2011-T2-2-042.\r\nK. Censor-Hillel is a Shalon Fellow. Part of this work was performed while K. Censor-Hillel was a postdoc at\r\nMIT, supported by the Simons Postdoctoral Fellowship." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Keren full_name: Censor Hillel, Keren last_name: Censor Hillel - first_name: Seth full_name: Gilbert, Seth last_name: Gilbert - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui citation: ama: Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Guerraoui R. Tight bounds for asynchronous renaming. Journal of the ACM. 2014;61(3). doi:10.1145/2597630 apa: Alistarh, D.-A., Aspnes, J., Censor Hillel, K., Gilbert, S., & Guerraoui, R. (2014). Tight bounds for asynchronous renaming. Journal of the ACM. ACM. https://doi.org/10.1145/2597630 chicago: Alistarh, Dan-Adrian, James Aspnes, Keren Censor Hillel, Seth Gilbert, and Rachid Guerraoui. “Tight Bounds for Asynchronous Renaming.” Journal of the ACM. ACM, 2014. https://doi.org/10.1145/2597630. ieee: D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, and R. Guerraoui, “Tight bounds for asynchronous renaming,” Journal of the ACM, vol. 61, no. 3. ACM, 2014. ista: Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Guerraoui R. 2014. Tight bounds for asynchronous renaming. Journal of the ACM. 61(3). mla: Alistarh, Dan-Adrian, et al. “Tight Bounds for Asynchronous Renaming.” Journal of the ACM, vol. 61, no. 3, ACM, 2014, doi:10.1145/2597630. short: D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, R. Guerraoui, Journal of the ACM 61 (2014). date_created: 2018-12-11T11:48:24Z date_published: 2014-05-01T00:00:00Z date_updated: 2023-02-23T13:14:09Z day: '01' doi: 10.1145/2597630 extern: '1' intvolume: ' 61' issue: '3' language: - iso: eng month: '05' oa_version: None publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '6887' status: public title: Tight bounds for asynchronous renaming type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2014' ... --- _id: '770' abstract: - lang: eng text: 'Dynamic memory reclamation is arguably the biggest open problem in concurrent data structure design: All known solutions induce high overhead, or must be customized to the specific data structure by the programmer, or both. This paper presents StackTrack, the first concurrent memory reclamation scheme that can be applied automatically by a compiler, while maintaining efficiency. StackTrack eliminates most of the expensive bookkeeping required for memory reclamation by leveraging the power of hardware transactional memory (HTM) in a new way: it tracks thread variables dynamically, and in an atomic fashion. This effectively makes all memory references visible without having threads pay the overhead of writing out this information. Our empirical results show that this new approach matches or outperforms prior, non-automated, techniques.' acknowledgement: "Dan Alistarh - Part of this work was performed while the \ author was a Postdoctoral\r\nAssociate a MIT CSAIL, supported in part by NSF grant CCF-1217921,\r\nDoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle\r\nand Intel corporations.\r\nPatrick Eugester - Supported in part by DARPA grant N11AP20014 and NSF grant CNS-\r\n1117065.\r\nMaurice Herlihy - Supported by NSF grant 1301924.\r\nNir Shavit - Supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and\r\nIntel corporations." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Patrick full_name: Eugster, Patrick last_name: Eugster - first_name: Maurice full_name: Herlihy, Maurice last_name: Herlihy - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. StackTrack: An automated transactional approach to concurrent memory reclamation. In: ACM; 2014. doi:10.1145/2592798.2592808' apa: 'Alistarh, D.-A., Eugster, P., Herlihy, M., Matveev, A., & Shavit, N. (2014). StackTrack: An automated transactional approach to concurrent memory reclamation. Presented at the EuroSys: European Conference on Computer Systems, ACM. https://doi.org/10.1145/2592798.2592808' chicago: 'Alistarh, Dan-Adrian, Patrick Eugster, Maurice Herlihy, Alexander Matveev, and Nir Shavit. “StackTrack: An Automated Transactional Approach to Concurrent Memory Reclamation.” ACM, 2014. https://doi.org/10.1145/2592798.2592808.' ieee: 'D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, and N. Shavit, “StackTrack: An automated transactional approach to concurrent memory reclamation,” presented at the EuroSys: European Conference on Computer Systems, 2014.' ista: 'Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. 2014. StackTrack: An automated transactional approach to concurrent memory reclamation. EuroSys: European Conference on Computer Systems.' mla: 'Alistarh, Dan-Adrian, et al. StackTrack: An Automated Transactional Approach to Concurrent Memory Reclamation. ACM, 2014, doi:10.1145/2592798.2592808.' short: D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, N. Shavit, in:, ACM, 2014. conference: name: 'EuroSys: European Conference on Computer Systems' date_created: 2018-12-11T11:48:24Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T13:14:25Z day: '01' doi: 10.1145/2592798.2592808 extern: '1' language: - iso: eng month: '01' oa_version: None publication_status: published publisher: ACM publist_id: '6888' status: public title: 'StackTrack: An automated transactional approach to concurrent memory reclamation' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '771' abstract: - lang: eng text: 'We consider the following natural problem: n failure-prone servers, communicating synchronously through message passing, must assign themselves one-to-one to n distinct items. Existing literature suggests two possible approaches to this problem. First, model it as an instance of tight renaming in synchronous message-passing systems; for deterministic solutions, a tight bound of ©(logn) communication rounds is known. Second, model the scenario as an instance of randomized load-balancing, for which elegant sub-logarithmic solutions exist. However, careful examination reveals that known load-balancing schemes do not apply to our scenario, because they either do not tolerate faults or do not ensure one-to-one allocation. It is thus natural to ask if sublogarithmic solutions exist for this apparently simple but intriguing problem. In this paper, we combine the two approaches to provide a new randomized solution for tight renaming, which terminates in O (log log n) communication rounds with high probability, against a strong adaptive adversary. Our solution, called Balls-into-Leaves, combines the deterministic approach with a new randomized scheme to obtain perfectly balanced allocations. The algorithm arranges the items as leaves of a tree, and participants repeatedly perform random choices among the leaves. The algorithm exchanges information in each round to split the participants into progressively smaller groups whose random choices do not conflict. We then extend the algorithm to terminate early in O(log log) rounds w.h.p., where is the actual number of failures. These results imply an exponential separation between deterministic and randomized algorithms for the tight renaming problem in message-passing systems.' acknowledgement: "Dan Alistarh was partially supported by the SNF Post-\r\ndoctoral Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from\r\nthe Oracle and Intel corporations.\r\nOksana Denysyuk and Lu ́ıs Rodrigues were partially supported by Funda ̧c ̃ao para a Ciˆencia e Tecnologia (FCT) via\r\nthe project PEPITA (PTDC/EEI-SCR/2776/2012) and via\r\nthe INESC-ID multi-annual funding through the PIDDAC\r\nProgram fund grant, under project PEst-OE/EEI/LA0021/\r\n2013.\r\nNir Shavit was supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Oksana full_name: Denysyuk, Oksana last_name: Denysyuk - first_name: Luís full_name: Rodrígues, Luís last_name: Rodrígues - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems. In: ACM; 2014:232-241. doi:10.1145/2611462.2611499' apa: 'Alistarh, D.-A., Denysyuk, O., Rodrígues, L., & Shavit, N. (2014). Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems (pp. 232–241). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2611462.2611499' chicago: 'Alistarh, Dan-Adrian, Oksana Denysyuk, Luís Rodrígues, and Nir Shavit. “Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems,” 232–41. ACM, 2014. https://doi.org/10.1145/2611462.2611499.' ieee: 'D.-A. Alistarh, O. Denysyuk, L. Rodrígues, and N. Shavit, “Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems,” presented at the PODC: Principles of Distributed Computing, 2014, pp. 232–241.' ista: 'Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. 2014. Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems. PODC: Principles of Distributed Computing, 232–241.' mla: 'Alistarh, Dan-Adrian, et al. Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems. ACM, 2014, pp. 232–41, doi:10.1145/2611462.2611499.' short: D.-A. Alistarh, O. Denysyuk, L. Rodrígues, N. Shavit, in:, ACM, 2014, pp. 232–241. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:25Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T13:14:49Z day: '01' doi: 10.1145/2611462.2611499 extern: '1' language: - iso: eng month: '01' oa_version: None page: 232 - 241 publication_status: published publisher: ACM publist_id: '6884' status: public title: 'Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '772' abstract: - lang: eng text: Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. While obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most non-blocking commercial code is only lock-free. This paper suggests a simple solution to this problem. We show that, for a large class of lock-free algorithms, under scheduling conditions which approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can keep on designing simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes with the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1, but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst case adversary, in a stochastic model capturing their expected asymptotic behavior. acknowledgement: "Dan Alistarh - Part of this work was performed while the author was a Postdoctoral Associate at MIT CSAIL, where he was supported by SNF\r\nPostdoctoral Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nKeron Censor-Hillel - Shalon Fellow\r\nNir Shavit - This work was supported in part by NSF grants CCF-1217921 and\r\nCCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and\r\nby grants from the Oracle and Intel corporations." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Keren full_name: Censor Hillel, Keren last_name: Censor Hillel - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Censor Hillel K, Shavit N. Are lock-free concurrent algorithms practically wait-free? In: ACM; 2014:714-723. doi:10.1145/2591796.2591836' apa: 'Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2014). Are lock-free concurrent algorithms practically wait-free? (pp. 714–723). Presented at the STOC: Symposium on Theory of Computing, ACM. https://doi.org/10.1145/2591796.2591836' chicago: Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock-Free Concurrent Algorithms Practically Wait-Free?,” 714–23. ACM, 2014. https://doi.org/10.1145/2591796.2591836. ieee: 'D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock-free concurrent algorithms practically wait-free?,” presented at the STOC: Symposium on Theory of Computing, 2014, pp. 714–723.' ista: 'Alistarh D-A, Censor Hillel K, Shavit N. 2014. Are lock-free concurrent algorithms practically wait-free? STOC: Symposium on Theory of Computing, 714–723.' mla: Alistarh, Dan-Adrian, et al. Are Lock-Free Concurrent Algorithms Practically Wait-Free? ACM, 2014, pp. 714–23, doi:10.1145/2591796.2591836. short: D.-A. Alistarh, K. Censor Hillel, N. Shavit, in:, ACM, 2014, pp. 714–723. conference: name: 'STOC: Symposium on Theory of Computing' date_created: 2018-12-11T11:48:25Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T13:15:13Z day: '01' doi: 10.1145/2591796.2591836 extern: '1' external_id: arxiv: - '1311.3200' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.3200 month: '01' oa: 1 oa_version: Preprint page: 714 - 723 publication_status: published publisher: ACM publist_id: '6885' status: public title: Are lock-free concurrent algorithms practically wait-free? type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '773' abstract: - lang: eng text: "We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n/2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(n log3n) messages in expectation, which is again within logarithmic factors of optimal.We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt + t2log2t) total messages. Our protocol uses messages of size O(log n), and can therefore scale to large networks.\r\n\r\nWe consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary.\r\n\r\nOur approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model." alternative_title: - LNCS article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: James full_name: Aspnes, James last_name: Aspnes - first_name: Valerie full_name: King, Valerie last_name: King - first_name: Jared full_name: Saia, Jared last_name: Saia citation: ama: 'Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. In: Kuhn F, ed. Vol 8784. Springer; 2014:61-75. doi:10.1007/978-3-662-45174-8_5' apa: 'Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2014). Communication-efficient randomized consensus. In F. Kuhn (Ed.) (Vol. 8784, pp. 61–75). Presented at the DISC: Distributed Computing, Austin, USA: Springer. https://doi.org/10.1007/978-3-662-45174-8_5' chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” edited by Fabian Kuhn, 8784:61–75. Springer, 2014. https://doi.org/10.1007/978-3-662-45174-8_5. ieee: 'D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” presented at the DISC: Distributed Computing, Austin, USA, 2014, vol. 8784, pp. 61–75.' ista: 'Alistarh D-A, Aspnes J, King V, Saia J. 2014. Communication-efficient randomized consensus. DISC: Distributed Computing, LNCS, vol. 8784, 61–75.' mla: Alistarh, Dan-Adrian, et al. Communication-Efficient Randomized Consensus. Edited by Fabian Kuhn, vol. 8784, Springer, 2014, pp. 61–75, doi:10.1007/978-3-662-45174-8_5. short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, in:, F. Kuhn (Ed.), Springer, 2014, pp. 61–75. conference: end_date: 2014-10-15 location: Austin, USA name: 'DISC: Distributed Computing' start_date: 2014-10-12 date_created: 2018-12-11T11:48:25Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T13:15:36Z day: '01' doi: 10.1007/978-3-662-45174-8_5 editor: - first_name: Fabian full_name: Kuhn, Fabian last_name: Kuhn extern: '1' intvolume: ' 8784' language: - iso: eng month: '01' oa_version: None page: 61 - 75 publication_status: published publisher: Springer publist_id: '6881' status: public title: Communication-efficient randomized consensus type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8784 year: '2014' ... --- _id: '774' abstract: - lang: eng text: Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers would prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is in general a complex undertaking, and the resulting algorithms are not always efficient, so most non-blocking commercial code is only lock-free, and the design of efficient wait-free algorithms has been left to the academic community. In [2], we suggest a solution to this problem. We show that, for a large class of lock-free algorithms, under scheduling conditions which approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can keep on designing simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes with the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1, but that in fact a broad subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. acknowledgement: "Dan Alistarh - Part of this work was performed while the \ author was a\r\nPostdoctoral Associate at MIT CSAIL, where he was supported \ by SNF Postdoctoral Fellows Program, NSF grant\r\nCCF-1217921, DoE ASCR grant ER26116/DE-SC0008923,\r\nand by grants from the Oracle and Intel corporations.\r\nKeren Censor-Hille - Shalon Fellow\r\nNir Shavit - This work was supported in part \ by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR grant ER26116/DE-\r\nSC0008923, and by grants from the Oracle and Intel corporations." article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Keren full_name: Censor Hille, Keren last_name: Censor Hille - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Censor Hille K, Shavit N. Brief announcement: Are lock-free concurrent algorithms practically wait-free? In: ACM; 2014:50-52. doi:10.1145/2611462.2611502' apa: 'Alistarh, D.-A., Censor Hille, K., & Shavit, N. (2014). Brief announcement: Are lock-free concurrent algorithms practically wait-free? (pp. 50–52). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2611462.2611502' chicago: 'Alistarh, Dan-Adrian, Keren Censor Hille, and Nir Shavit. “Brief Announcement: Are Lock-Free Concurrent Algorithms Practically Wait-Free?,” 50–52. ACM, 2014. https://doi.org/10.1145/2611462.2611502.' ieee: 'D.-A. Alistarh, K. Censor Hille, and N. Shavit, “Brief announcement: Are lock-free concurrent algorithms practically wait-free?,” presented at the PODC: Principles of Distributed Computing, 2014, pp. 50–52.' ista: 'Alistarh D-A, Censor Hille K, Shavit N. 2014. Brief announcement: Are lock-free concurrent algorithms practically wait-free? PODC: Principles of Distributed Computing, 50–52.' mla: 'Alistarh, Dan-Adrian, et al. Brief Announcement: Are Lock-Free Concurrent Algorithms Practically Wait-Free? ACM, 2014, pp. 50–52, doi:10.1145/2611462.2611502.' short: D.-A. Alistarh, K. Censor Hille, N. Shavit, in:, ACM, 2014, pp. 50–52. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:26Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T13:15:54Z day: '01' doi: 10.1145/2611462.2611502 extern: '1' language: - iso: eng month: '01' oa_version: None page: 50 - 52 publication_status: published publisher: ACM publist_id: '6882' status: public title: 'Brief announcement: Are lock-free concurrent algorithms practically wait-free?' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '775' abstract: - lang: eng text: 'The long-lived renaming problem appears in shared-memory systems where a set of threads need to register and deregister frequently from the computation, while concurrent operations scan the set of currently registered threads. Instances of this problem show up in concurrent implementations of transactional memory, flat combining, thread barriers, and memory reclamation schemes for lock-free data structures. In this paper, we analyze a randomized solution for long-lived renaming. The algorithmic technique we consider, called the Level Array, has previously been used for hashing and one-shot (single-use) renaming. Our main contribution is to prove that, in long-lived executions, where processes may register and deregister polynomially many times, the technique guarantees constant steps on average and O (log log n) steps with high probability for registering, unit cost for deregistering, and O (n) steps for collect queries, where n is an upper bound on the number of processes that may be active at any point in time. We also show that the algorithm has the surprising property that it is self-healing: under reasonable assumptions on the schedule, operations running while the data structure is in a degraded state implicitly help the data structure re-balance itself. This subtle mechanism obviates the need for expensive periodic rebuilding procedures. Our benchmarks validate this approach, showing that, for typical use parameters, the average number of steps a process takes to register is less than two and the worst-case number of steps is bounded by six, even in executions with billions of operations. We contrast this with other randomized implementations, whose worst-case behavior we show to be unreliable, and with deterministic implementations, whose cost is linear in n.' article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: Nir full_name: Shavit, Nir last_name: Shavit citation: ama: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. The levelarray: A fast, practical long-lived renaming algorithm. In: IEEE; 2014:348-357. doi:10.1109/ICDCS.2014.43' apa: 'Alistarh, D.-A., Kopinsky, J., Matveev, A., & Shavit, N. (2014). The levelarray: A fast, practical long-lived renaming algorithm (pp. 348–357). Presented at the ICDCS: International Conference on Distributed Computing Systems, IEEE. https://doi.org/10.1109/ICDCS.2014.43' chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Alexander Matveev, and Nir Shavit. “The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm,” 348–57. IEEE, 2014. https://doi.org/10.1109/ICDCS.2014.43.' ieee: 'D.-A. Alistarh, J. Kopinsky, A. Matveev, and N. Shavit, “The levelarray: A fast, practical long-lived renaming algorithm,” presented at the ICDCS: International Conference on Distributed Computing Systems, 2014, pp. 348–357.' ista: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. 2014. The levelarray: A fast, practical long-lived renaming algorithm. ICDCS: International Conference on Distributed Computing Systems, 348–357.' mla: 'Alistarh, Dan-Adrian, et al. The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm. IEEE, 2014, pp. 348–57, doi:10.1109/ICDCS.2014.43.' short: D.-A. Alistarh, J. Kopinsky, A. Matveev, N. Shavit, in:, IEEE, 2014, pp. 348–357. conference: name: 'ICDCS: International Conference on Distributed Computing Systems' date_created: 2018-12-11T11:48:26Z date_published: 2014-08-29T00:00:00Z date_updated: 2023-02-23T13:16:18Z day: '29' doi: 10.1109/ICDCS.2014.43 extern: '1' external_id: arxiv: - '1405.5461' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1405.5461 month: '08' oa: 1 oa_version: Preprint page: 348 - 357 publication_status: published publisher: IEEE publist_id: '6883' status: public title: 'The levelarray: A fast, practical long-lived renaming algorithm' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '7743' abstract: - lang: eng text: Experimental studies have demonstrated that environmental variation can create genotype‐environment interactions (GEIs) in the traits involved in sexual selection. Understanding the genetic architecture of phenotype across environments will require statistical tests that can describe both changes in genetic variance and covariance across environments. This chapter outlines the theoretical framework for the processes of sexual selection in the wild, identifying key parameters in wild systems, and highlighting the potential effects of the environment. It describes the proposed approaches for the estimation of these key parameters in a quantitative genetic framework within naturally occurring pedigreed populations. The chapter provides a worked example for a range of analysis methods. It aims to provide an overview of the analytical methods that can be used to model GEIs for traits involved in sexual selection in naturally occurring pedigreed populations. article_processing_charge: No author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Anna full_name: Qvarnström, Anna last_name: Qvarnström citation: ama: 'Robinson MR, Qvarnström A. Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In: Hunt J, Hosken D, eds. Genotype-by-Environment Interactions and Sexual Selection. Chichester, UK: Wiley; 2014:137-168. doi:10.1002/9781118912591.ch6' apa: 'Robinson, M. R., & Qvarnström, A. (2014). Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In J. Hunt & D. Hosken (Eds.), Genotype-by-Environment Interactions and Sexual Selection (pp. 137–168). Chichester, UK: Wiley. https://doi.org/10.1002/9781118912591.ch6' chicago: 'Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment on the Genetic Architecture of Traits Involved in Sexual Selection within Wild Populations.” In Genotype-by-Environment Interactions and Sexual Selection, edited by John Hunt and David Hosken, 137–68. Chichester, UK: Wiley, 2014. https://doi.org/10.1002/9781118912591.ch6.' ieee: 'M. R. Robinson and A. Qvarnström, “Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations,” in Genotype-by-Environment Interactions and Sexual Selection, J. Hunt and D. Hosken, Eds. Chichester, UK: Wiley, 2014, pp. 137–168.' ista: 'Robinson MR, Qvarnström A. 2014.Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In: Genotype-by-Environment Interactions and Sexual Selection. , 137–168.' mla: Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment on the Genetic Architecture of Traits Involved in Sexual Selection within Wild Populations.” Genotype-by-Environment Interactions and Sexual Selection, edited by John Hunt and David Hosken, Wiley, 2014, pp. 137–68, doi:10.1002/9781118912591.ch6. short: M.R. Robinson, A. Qvarnström, in:, J. Hunt, D. Hosken (Eds.), Genotype-by-Environment Interactions and Sexual Selection, Wiley, Chichester, UK, 2014, pp. 137–168. date_created: 2020-04-30T10:58:39Z date_published: 2014-08-29T00:00:00Z date_updated: 2021-01-12T08:15:13Z day: '29' doi: 10.1002/9781118912591.ch6 editor: - first_name: John full_name: Hunt, John last_name: Hunt - first_name: David full_name: Hosken, David last_name: Hosken extern: '1' language: - iso: eng month: '08' oa_version: None page: 137-168 place: Chichester, UK publication: Genotype-by-Environment Interactions and Sexual Selection publication_identifier: eisbn: - '9781118912591' isbn: - '9780470671795' publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '7744' article_processing_charge: No article_type: original author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher citation: ama: Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation in complex traits. Trends in Genetics. 2014;30(4):124-132. doi:10.1016/j.tig.2014.02.003 apa: Robinson, M. R., Wray, N. R., & Visscher, P. M. (2014). Explaining additional genetic variation in complex traits. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.02.003 chicago: Robinson, Matthew Richard, Naomi R. Wray, and Peter M. Visscher. “Explaining Additional Genetic Variation in Complex Traits.” Trends in Genetics. Elsevier, 2014. https://doi.org/10.1016/j.tig.2014.02.003. ieee: M. R. Robinson, N. R. Wray, and P. M. Visscher, “Explaining additional genetic variation in complex traits,” Trends in Genetics, vol. 30, no. 4. Elsevier, pp. 124–132, 2014. ista: Robinson MR, Wray NR, Visscher PM. 2014. Explaining additional genetic variation in complex traits. Trends in Genetics. 30(4), 124–132. mla: Robinson, Matthew Richard, et al. “Explaining Additional Genetic Variation in Complex Traits.” Trends in Genetics, vol. 30, no. 4, Elsevier, 2014, pp. 124–32, doi:10.1016/j.tig.2014.02.003. short: M.R. Robinson, N.R. Wray, P.M. Visscher, Trends in Genetics 30 (2014) 124–132. date_created: 2020-04-30T10:58:58Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T08:15:14Z day: '01' doi: 10.1016/j.tig.2014.02.003 extern: '1' intvolume: ' 30' issue: '4' language: - iso: eng month: '04' oa_version: None page: 124-132 publication: Trends in Genetics publication_identifier: issn: - 0168-9525 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Explaining additional genetic variation in complex traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2014' ... --- _id: '7768' abstract: - lang: eng text: We investigate the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions as a function of packing fraction. Certain properties of the vibrational density of states (vDOS) are shown to correlate with the density and structure of the samples (i.e., in sparsely versus densely packed samples). Specifically, a crossover from dense glassy to sparse gel-like states is suggested by an excess of phonon modes at low frequency and by a variation in the slope of the vDOS with frequency at low frequency. This change in phonon mode distribution is demonstrated to arise largely from localized vibrations that involve individual and/or small clusters of particles with few local bonds. Conventional order parameters and void statistics did not exhibit obvious gel-glass signatures as a function of volume fraction. These mode behaviors and accompanying structural insights offer a potentially new set of indicators for identification of glass-gel transitions and for assignment of gel-like versus glass-like character to a disordered solid material. article_number: '062305' article_processing_charge: No article_type: original author: - first_name: Matthew A. full_name: Lohr, Matthew A. last_name: Lohr - first_name: Tim full_name: Still, Tim last_name: Still - first_name: Raman full_name: Ganti, Raman last_name: Ganti - first_name: Matthew D. full_name: Gratale, Matthew D. last_name: Gratale - first_name: Zoey S. full_name: Davidson, Zoey S. last_name: Davidson - first_name: Kevin B. full_name: Aptowicz, Kevin B. last_name: Aptowicz - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Daniel M. full_name: Sussman, Daniel M. last_name: Sussman - first_name: A. G. full_name: Yodh, A. G. last_name: Yodh citation: ama: Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. 2014;90(6). doi:10.1103/physreve.90.062305 apa: Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz, K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.062305 chicago: Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson, Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.90.062305. ieee: M. A. Lohr et al., “Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings,” Physical Review E, vol. 90, no. 6. American Physical Society, 2014. ista: Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. 90(6), 062305. mla: Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” Physical Review E, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:10.1103/physreve.90.062305. short: M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz, C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014). date_created: 2020-04-30T11:41:54Z date_published: 2014-12-05T00:00:00Z date_updated: 2021-01-12T08:15:24Z day: '05' doi: 10.1103/physreve.90.062305 extern: '1' intvolume: ' 90' issue: '6' language: - iso: eng month: '12' oa_version: None publication: Physical Review E publication_identifier: issn: - 1539-3755 - 1550-2376 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 90 year: '2014' ... --- _id: '7771' abstract: - lang: eng text: 'In their Letter, Schreck, Bertrand, O''Hern and Shattuck [Phys. Rev. Lett. 107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise when contacts are altered. They conclude that there is "no harmonic regime in the large system limit for all compressions" and "at jamming onset for any system size." Their argument rests on the claim that for finite-range repulsive potentials, of the form used in studies of jamming, the breaking or forming of a single contact is sufficient to destroy the linear regime. We dispute these conclusions and argue that linear response is both justified and essential for understanding the nature of the jammed solid. ' article_number: '049801 ' article_processing_charge: No article_type: letter_note author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” Physical Review Letters. 2014;112(4). doi:10.1103/physrevlett.112.049801 apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.112.049801 chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.112.049801. ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact interactions make jammed particulate systems inherently nonharmonic,’” Physical Review Letters, vol. 112, no. 4. American Physical Society, 2014. ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”. Physical Review Letters. 112(4), 049801. mla: Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters, vol. 112, no. 4, 049801, American Physical Society, 2014, doi:10.1103/physrevlett.112.049801. short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014). date_created: 2020-04-30T11:42:39Z date_published: 2014-04-20T00:00:00Z date_updated: 2021-01-12T08:15:26Z day: '20' doi: 10.1103/physrevlett.112.049801 extern: '1' external_id: arxiv: - '1306.1285' intvolume: ' 112' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1306.1285 month: '04' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society status: public title: Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic” type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2014' ... --- _id: '7772' abstract: - lang: eng text: Particle tracking and displacement covariance matrix techniques are employed to investigate the phonon dispersion relations of two-dimensional colloidal glasses composed of soft, thermoresponsive microgel particles whose temperature-sensitive size permits in situ variation of particle packing fraction. Bulk, B, and shear, G, moduli of the colloidal glasses are extracted from the dispersion relations as a function of packing fraction, and variation of the ratio G/B with packing fraction is found to agree quantitatively with predictions for jammed packings of frictional soft particles. In addition, G and B individually agree with numerical predictions for frictional particles. This remarkable level of agreement enabled us to extract an energy scale for the interparticle interaction from the individual elastic constants and to derive an approximate estimate for the interparticle friction coefficient. article_number: '012301' article_processing_charge: No article_type: original author: - first_name: Tim full_name: Still, Tim last_name: Still - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Ke full_name: Chen, Ke last_name: Chen - first_name: Peter J. full_name: Yunker, Peter J. last_name: Yunker - first_name: Samuel full_name: Schoenholz, Samuel last_name: Schoenholz - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: A. G. full_name: Yodh, A. G. last_name: Yodh citation: ama: Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. Physical Review E. 2014;89(1). doi:10.1103/physreve.89.012301 apa: Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A. J., & Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.012301 chicago: Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz, Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.012301. ieee: T. Still et al., “Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions,” Physical Review E, vol. 89, no. 1. American Physical Society, 2014. ista: Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. Physical Review E. 89(1), 012301. mla: Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” Physical Review E, vol. 89, no. 1, 012301, American Physical Society, 2014, doi:10.1103/physreve.89.012301. short: T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G. Yodh, Physical Review E 89 (2014). date_created: 2020-04-30T11:43:02Z date_published: 2014-01-03T00:00:00Z date_updated: 2021-01-12T08:15:26Z day: '03' doi: 10.1103/physreve.89.012301 extern: '1' intvolume: ' 89' issue: '1' language: - iso: eng month: '01' oa_version: None publication: Physical Review E publication_identifier: issn: - 1539-3755 - 1550-2376 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '7773' abstract: - lang: eng text: 'For more than a century, physicists have described real solids in terms of perturbations about perfect crystalline order1. Such an approach takes us only so far: a glass, another ubiquitous form of rigid matter, cannot be described in any meaningful sense as a defected crystal2. Is there an opposite extreme to a crystal—a solid with complete disorder—that forms an alternative starting point for understanding real materials? Here, we argue that the solid comprising particles with finite-ranged interactions at the jamming transition3,4,5 constitutes such a limit. It has been shown that the physics associated with this transition can be extended to interactions that are long ranged6. We demonstrate that jamming physics is not restricted to amorphous systems, but dominates the behaviour of solids with surprisingly high order. Just as the free-electron and tight-binding models represent two idealized cases from which to understand electronic structure1, we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming can be set side by side with the physics of crystals to provide an organizing structure for understanding the mechanical properties of solids over the entire spectrum of disorder.' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order and disorder. Nature Physics. 2014;10(8):578-581. doi:10.1038/nphys3006 apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Solids between the mechanical extremes of order and disorder. Nature Physics. Springer Nature. https://doi.org/10.1038/nphys3006 chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between the Mechanical Extremes of Order and Disorder.” Nature Physics. Springer Nature, 2014. https://doi.org/10.1038/nphys3006. ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical extremes of order and disorder,” Nature Physics, vol. 10, no. 8. Springer Nature, pp. 578–581, 2014. ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes of order and disorder. Nature Physics. 10(8), 578–581. mla: Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order and Disorder.” Nature Physics, vol. 10, no. 8, Springer Nature, 2014, pp. 578–81, doi:10.1038/nphys3006. short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581. date_created: 2020-04-30T11:43:29Z date_published: 2014-07-06T00:00:00Z date_updated: 2021-01-12T08:15:26Z day: '06' doi: 10.1038/nphys3006 extern: '1' intvolume: ' 10' issue: '8' language: - iso: eng month: '07' oa_version: None page: 578-581 publication: Nature Physics publication_identifier: issn: - 1745-2473 - 1745-2481 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Solids between the mechanical extremes of order and disorder type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2014' ... --- _id: '7769' abstract: - lang: eng text: 'Athermal packings of soft repulsive spheres exhibit a sharp jamming transition in the thermodynamic limit. Upon further compression, various structural and mechanical properties display clean power-law behavior over many decades in pressure. As with any phase transition, the rounding of such behavior in finite systems close to the transition plays an important role in understanding the nature of the transition itself. The situation for jamming is surprisingly rich: the assumption that jammed packings are isotropic is only strictly true in the large-size limit, and finite-size has a profound effect on the very meaning of jamming. Here, we provide a comprehensive numerical study of finite-size effects in sphere packings above the jamming transition, focusing on stability as well as the scaling of the contact number and the elastic response.' article_number: '022138' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Simon full_name: Dagois-Bohy, Simon last_name: Dagois-Bohy - first_name: Brian P. full_name: Tighe, Brian P. last_name: Tighe - first_name: Martin full_name: van Hecke, Martin last_name: van Hecke - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical Review E. 2014;90(2). doi:10.1103/physreve.90.022138' apa: 'Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J., & Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.022138' chicago: 'Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke, Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.90.022138.' ieee: 'C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling,” Physical Review E, vol. 90, no. 2. American Physical Society, 2014.' ista: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical Review E. 90(2), 022138.' mla: 'Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” Physical Review E, vol. 90, no. 2, 022138, American Physical Society, 2014, doi:10.1103/physreve.90.022138.' short: C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014). date_created: 2020-04-30T11:42:09Z date_published: 2014-08-27T00:00:00Z date_updated: 2021-01-12T08:15:24Z day: '27' doi: 10.1103/physreve.90.022138 extern: '1' intvolume: ' 90' issue: '2' language: - iso: eng month: '08' oa_version: None publication: Physical Review E publication_identifier: issn: - 1539-3755 - 1550-2376 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: 'Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 90 year: '2014' ... --- _id: '7770' abstract: - lang: eng text: Packings of frictionless athermal particles that interact only when they overlap experience a jamming transition as a function of packing density. Such packings provide the foundation for the theory of jamming. This theory rests on the observation that, despite the multitude of disordered configurations, the mechanical response to linear order depends only on the distance to the transition. We investigate the validity and utility of such measurements that invoke the harmonic approximation and show that, despite particles coming in and out of contact, there is a well-defined linear regime in the thermodynamic limit. article_number: '022201' article_processing_charge: No article_type: original author: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu - first_name: Sidney R. full_name: Nagel, Sidney R. last_name: Nagel citation: ama: Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in jammed particulate packings. Physical Review E. 2014;90(2). doi:10.1103/physreve.90.022201 apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Contact nonlinearities and linear response in jammed particulate packings. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.022201 chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.90.022201. ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear response in jammed particulate packings,” Physical Review E, vol. 90, no. 2. American Physical Society, 2014. ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response in jammed particulate packings. Physical Review E. 90(2), 022201. mla: Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” Physical Review E, vol. 90, no. 2, 022201, American Physical Society, 2014, doi:10.1103/physreve.90.022201. short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014). date_created: 2020-04-30T11:42:24Z date_published: 2014-08-04T00:00:00Z date_updated: 2021-01-12T08:15:25Z day: '04' doi: 10.1103/physreve.90.022201 extern: '1' intvolume: ' 90' issue: '2' language: - iso: eng month: '08' oa_version: None publication: Physical Review E publication_identifier: issn: - 1539-3755 - 1550-2376 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Contact nonlinearities and linear response in jammed particulate packings type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 90 year: '2014' ... --- _id: '8021' abstract: - lang: eng text: 'Most excitatory inputs in the mammalian brain are made on dendritic spines, rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical isolation can underlie input-specific synaptic plasticity, providing a raison d''etre for spines. However, recent results indicate that the spine can experience a membrane potential different from that in the parent dendrite, as though the spine neck electrically isolated the spine. Here we use two-photon calcium imaging of mouse neocortical pyramidal neurons to analyze the correlation between the morphologies of spines activated under minimal synaptic stimulation and the excitatory postsynaptic potentials they generate. We find that excitatory postsynaptic potential amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike timing-dependent plasticity protocol, in which two-photon glutamate uncaging over a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine neck and concomitant increases in the amplitude of the evoked spine potentials. Using numerical simulations, we explore the parameter regimes for the spine neck resistance and synaptic conductance changes necessary to explain our observations. Our data, directly correlating synaptic and morphological plasticity, imply that long-necked spines have small or negligible somatic voltage contributions, but that, upon synaptic stimulation paired with postsynaptic activity, they can shorten their necks and increase synaptic efficacy, thus changing the input/output gain of pyramidal neurons. ' article_processing_charge: No article_type: original author: - first_name: R. full_name: Araya, R. last_name: Araya - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: R. full_name: Yuste, R. last_name: Yuste citation: ama: Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. Proceedings of the National Academy of Sciences. 2014;111(28):E2895-E2904. doi:10.1073/pnas.1321869111 apa: Araya, R., Vogels, T. P., & Yuste, R. (2014). Activity-dependent dendritic spine neck changes are correlated with synaptic strength. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1321869111 chicago: Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1321869111. ieee: R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine neck changes are correlated with synaptic strength,” Proceedings of the National Academy of Sciences, vol. 111, no. 28. Proceedings of the National Academy of Sciences, pp. E2895–E2904, 2014. ista: Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. Proceedings of the National Academy of Sciences. 111(28), E2895–E2904. mla: Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National Academy of Sciences, vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904, doi:10.1073/pnas.1321869111. short: R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences 111 (2014) E2895–E2904. date_created: 2020-06-25T13:06:24Z date_published: 2014-07-15T00:00:00Z date_updated: 2021-01-12T08:16:34Z day: '15' doi: 10.1073/pnas.1321869111 extern: '1' external_id: pmid: - '24982196' intvolume: ' 111' issue: '28' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/ month: '07' oa: 1 oa_version: Published Version page: E2895-E2904 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: Activity-dependent dendritic spine neck changes are correlated with synaptic strength type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 111 year: '2014' ... --- _id: '8023' abstract: - lang: eng text: Uniform random sparse network architectures are ubiquitous in computational neuroscience, but the implicit hypothesis that they are a good representation of real neuronal networks has been met with skepticism. Here we used two experimental data sets, a study of triplet connectivity statistics and a data set measuring neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands of model networks. Network architectures comprised three neuron types (excitatory, fast spiking, and nonfast spiking inhibitory) and were created from a set of rules that govern the statistics of the resulting connection types. In a high-dimensional parameter scan, we varied the degree distributions (i.e., how many cells each neuron connects with) and the synaptic weight correlations of synapses from or onto the same neuron. These variations converted initially uniform random and homogeneously connected networks, in which every neuron sent and received equal numbers of synapses with equal synaptic strength distributions, to highly heterogeneous networks in which the number of synapses per neuron, as well as average synaptic strength of synapses from or to a neuron were variable. By evaluating the impact of each variable on the network structure and dynamics, and their similarity to the experimental data, we could falsify the uniform random sparse connectivity hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis in 8 cases. Twenty-one parameters had no substantial impact on the results of the test protocols we used. article_processing_charge: No article_type: original author: - first_name: Christian full_name: Tomm, Christian last_name: Tomm - first_name: Michael full_name: Avermann, Michael last_name: Avermann - first_name: Carl full_name: Petersen, Carl last_name: Petersen - first_name: Wulfram full_name: Gerstner, Wulfram last_name: Gerstner - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific biases make uniform random network models consistent with cortical recordings. Journal of Neurophysiology. 2014;112(8):1801-1814. doi:10.1152/jn.00629.2013 apa: Tomm, C., Avermann, M., Petersen, C., Gerstner, W., & Vogels, T. P. (2014). Connection-type-specific biases make uniform random network models consistent with cortical recordings. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00629.2013 chicago: Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” Journal of Neurophysiology. American Physiological Society, 2014. https://doi.org/10.1152/jn.00629.2013. ieee: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific biases make uniform random network models consistent with cortical recordings,” Journal of Neurophysiology, vol. 112, no. 8. American Physiological Society, pp. 1801–1814, 2014. ista: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific biases make uniform random network models consistent with cortical recordings. Journal of Neurophysiology. 112(8), 1801–1814. mla: Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” Journal of Neurophysiology, vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:10.1152/jn.00629.2013. short: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology 112 (2014) 1801–1814. date_created: 2020-06-25T13:08:30Z date_published: 2014-10-15T00:00:00Z date_updated: 2021-01-12T08:16:35Z day: '15' ddc: - '570' doi: 10.1152/jn.00629.2013 extern: '1' external_id: pmid: - '24944218' file: - access_level: open_access checksum: 7c06a086da6f924342650de6dc555c3f content_type: application/pdf creator: cziletti date_created: 2020-07-16T10:12:13Z date_updated: 2020-07-16T10:12:13Z file_id: '8122' file_name: 2014_JNeurophysiol_Tomm.pdf file_size: 1632295 relation: main_file success: 1 file_date_updated: 2020-07-16T10:12:13Z has_accepted_license: '1' intvolume: ' 112' issue: '8' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '10' oa: 1 oa_version: Published Version page: 1801-1814 pmid: 1 publication: Journal of Neurophysiology publication_identifier: eissn: - 1522-1598 issn: - 0022-3077 publication_status: published publisher: American Physiological Society quality_controlled: '1' status: public title: Connection-type-specific biases make uniform random network models consistent with cortical recordings 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: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 112 year: '2014' ... --- _id: '8022' abstract: - lang: eng text: Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex. article_processing_charge: No article_type: original author: - first_name: Guillaume full_name: Hennequin, Guillaume last_name: Hennequin - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Wulfram full_name: Gerstner, Wulfram last_name: Gerstner citation: ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406. doi:10.1016/j.neuron.2014.04.045 apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045 chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045. ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient dynamics in balanced networks supports generation of complex movements,” Neuron, vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014. ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 82(6), 1394–1406. mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045. short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406. date_created: 2020-06-25T13:07:37Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T08:16:35Z day: '18' doi: 10.1016/j.neuron.2014.04.045 extern: '1' external_id: pmid: - '24945778' intvolume: ' 82' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/ month: '06' oa: 1 oa_version: Submitted Version page: 1394-1406 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Optimal control of transient dynamics in balanced networks supports generation of complex movements type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 82 year: '2014' ... --- _id: '809' abstract: - lang: eng text: The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position. acknowledgement: 'The authors thank Leonardo Trabuco for help with running MDFF, Maria Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber (robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal screening, and the European Molecular Biology Laboratory (EMBL) Information Technology Services Unit and Frank Thommen for technical support. This study was supported by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship (to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL and the Chica und Heinz Schaller Stiftung. ' author: - first_name: Tanmay full_name: Bharata, Tanmay A last_name: Bharata - first_name: Luis full_name: Menendez, Luis R last_name: Menendez - first_name: Wim full_name: Hagena, Wim J last_name: Hagena - first_name: Vanda full_name: Luxd, Vanda last_name: Luxd - first_name: Sebastien full_name: Igonete, Sebastien last_name: Igonete - first_name: Martin full_name: Schorba, Martin last_name: Schorba - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Hans full_name: Kraüsslich, Hans Georg last_name: Kraüsslich - first_name: John full_name: Briggsa, John A last_name: Briggsa citation: ama: Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 2014;111(22):8233-8238. doi:10.1073/pnas.1401455111 apa: Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M., … Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1401455111 chicago: Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete, Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1401455111. ieee: T. Bharata et al., “Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly,” PNAS, vol. 111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014. ista: Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 111(22), 8233–8238. mla: Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS, vol. 111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:10.1073/pnas.1401455111. short: T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K. Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238. date_created: 2018-12-11T11:48:37Z date_published: 2014-06-03T00:00:00Z date_updated: 2021-01-12T08:16:50Z day: '03' doi: 10.1073/pnas.1401455111 extern: 1 intvolume: ' 111' issue: '22' month: '06' page: 8233 - 8238 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6838' quality_controlled: 0 status: public title: Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 111 year: '2014' ... --- _id: '8244' abstract: - lang: eng text: Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer. article_processing_charge: No article_type: original author: - first_name: J. full_name: Singer, J. last_name: Singer - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: W. full_name: Wang, W. last_name: Wang - first_name: M. full_name: Weichselbaumer, M. last_name: Weichselbaumer - first_name: M. full_name: Matz, M. last_name: Matz - first_name: A. full_name: Mader, A. last_name: Mader - first_name: W. full_name: Steinfellner, W. last_name: Steinfellner - first_name: S. full_name: Meitz, S. last_name: Meitz - first_name: D. full_name: Mechtcheriakova, D. last_name: Mechtcheriakova - first_name: Y. full_name: Sobanov, Y. last_name: Sobanov - first_name: M. full_name: Willmann, M. last_name: Willmann - first_name: T. full_name: Stockner, T. last_name: Stockner - first_name: E. full_name: Spillner, E. last_name: Spillner - first_name: R. full_name: Kunert, R. last_name: Kunert - first_name: E. full_name: Jensen-Jarolim, E. last_name: Jensen-Jarolim citation: ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288 apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A., … Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288 chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics. American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288. ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics, vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014. ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E, Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 13(7), 1777–1790. mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics, vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288. short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner, R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790. date_created: 2020-08-10T11:54:29Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T08:17:42Z day: '01' doi: 10.1158/1535-7163.mct-13-0288 extern: '1' intvolume: ' 13' issue: '7' language: - iso: eng month: '07' oa_version: None page: 1777-1790 publication: Molecular Cancer Therapeutics publication_identifier: issn: - 1535-7163 - 1538-8514 publication_status: published publisher: American Association for Cancer Research quality_controlled: '1' status: public title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2014' ... --- _id: '8459' abstract: - lang: eng text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis. article_processing_charge: No article_type: original author: - first_name: Sébastien full_name: Morin, Sébastien last_name: Morin - first_name: Troels E full_name: Linnet, Troels E last_name: Linnet - first_name: Mathilde full_name: Lescanne, Mathilde last_name: Lescanne - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Gary S full_name: Thompson, Gary S last_name: Thompson - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger - first_name: Kaare full_name: Teilum, Kaare last_name: Teilum - first_name: Stéphane full_name: Gagné, Stéphane last_name: Gagné - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Christian full_name: Griesinger, Christian last_name: Griesinger - first_name: Martin full_name: Blackledge, Martin last_name: Blackledge - first_name: Edward J full_name: d’Auvergne, Edward J last_name: d’Auvergne citation: ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166' apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btu166' chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics. Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.' ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.' ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.' mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.' short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220. date_created: 2020-09-18T10:08:07Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/bioinformatics/btu166 extern: '1' intvolume: ' 30' issue: '15' keyword: - Statistics and Probability - Computational Theory and Mathematics - Biochemistry - Molecular Biology - Computational Mathematics - Computer Science Applications language: - iso: eng month: '08' oa_version: None page: 2219-2220 publication: Bioinformatics publication_identifier: issn: - 1367-4803 - 1460-2059 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/bioinformatics/btz397 status: public title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2014' ... --- _id: '8458' abstract: - lang: eng text: The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Sébastien full_name: Triboulet, Sébastien last_name: Triboulet - first_name: Cédric full_name: Laguri, Cédric last_name: Laguri - first_name: Catherine M. full_name: Bougault, Catherine M. last_name: Bougault - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Morgane full_name: Callon, Morgane last_name: Callon - first_name: Michel full_name: Arthur, Michel last_name: Arthur - first_name: Jean-Pierre full_name: Simorre, Jean-Pierre last_name: Simorre citation: ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987 apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon, M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987 chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical Society. American Chemical Society, 2014. https://doi.org/10.1021/ja5105987. ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan,” Journal of the American Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860, 2014. ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 136(51), 17852–17860. mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60, doi:10.1021/ja5105987. short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon, M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014) 17852–17860. date_created: 2020-09-18T10:07:52Z date_published: 2014-11-27T00:00:00Z date_updated: 2021-01-12T08:19:24Z day: '27' doi: 10.1021/ja5105987 extern: '1' intvolume: ' 136' issue: '51' language: - iso: eng month: '11' oa_version: None page: 17852-17860 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2014' ... --- _id: '8460' abstract: - lang: eng text: The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states. article_processing_charge: No article_type: original author: - first_name: Peixiang full_name: Ma, Peixiang last_name: Ma - first_name: Jens D. full_name: Haller, Jens D. last_name: Haller - first_name: Jérémy full_name: Zajakala, Jérémy last_name: Zajakala - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Dieter full_name: Willbold, Dieter last_name: Willbold - first_name: Jérôme full_name: Boisbouvier, Jérôme last_name: Boisbouvier - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275 apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201311275 chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275. ieee: P. Ma et al., “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014. ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317. mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275. short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317. date_created: 2020-09-18T10:08:53Z date_published: 2014-03-18T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '18' doi: 10.1002/anie.201311275 extern: '1' intvolume: ' 53' issue: '17' language: - iso: eng month: '03' oa_version: None page: 4312-4317 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2014' ... --- _id: '8501' abstract: - lang: eng text: In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation. article_processing_charge: No article_type: original author: - first_name: Abed full_name: Bounemoura, Abed last_name: Bounemoura - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203 apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203 chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203. ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014. ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203. mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203. short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203. date_created: 2020-09-18T10:47:09Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T08:19:43Z day: '01' doi: 10.17323/1609-4514-2014-14-2-181-203 extern: '1' external_id: arxiv: - '1304.3050' intvolume: ' 14' issue: '2' keyword: - General Mathematics language: - iso: eng month: '04' oa_version: Preprint page: 181-203 publication: Moscow Mathematical Journal publication_identifier: issn: - 1609-3321 - 1609-4514 publication_status: published publisher: Independent University of Moscow quality_controlled: '1' status: public title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '8500' abstract: - lang: eng text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way. article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Mark full_name: Levi, Mark last_name: Levi - first_name: Maria full_name: Saprykina, Maria last_name: Saprykina citation: ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509 apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21509 chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley, 2014. https://doi.org/10.1002/cpa.21509. ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley, pp. 748–775, 2014. ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775. mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:10.1002/cpa.21509. short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775. date_created: 2020-09-18T10:47:01Z date_published: 2014-05-01T00:00:00Z date_updated: 2022-08-25T13:58:13Z day: '01' doi: 10.1002/cpa.21509 extern: '1' intvolume: ' 67' issue: '5' keyword: - Applied Mathematics - General Mathematics language: - iso: eng month: '05' oa_version: None page: 748-775 publication: Communications on Pure and Applied Mathematics publication_identifier: issn: - 0010-3640 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Arnol′d diffusion in a pendulum lattice type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 67 year: '2014' ... --- _id: '852' abstract: - lang: eng text: 'Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. ' author: - first_name: Oriol full_name: Rosello, Oriol P last_name: Rosello - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955. doi:10.1093/gbe/evu159 apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evu159 chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159. ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” Genome Biology and Evolution, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014. ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955. mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159. short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955. date_created: 2018-12-11T11:48:51Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:51Z day: '01' doi: 10.1093/gbe/evu159 extern: 1 intvolume: ' 6' issue: '8' month: '08' page: 1949 - 1955 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6797' quality_controlled: 0 status: public title: Long-Term asymmetrical acceleration of protein evolution after gene duplication tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2014' ... --- _id: '856' abstract: - lang: eng text: The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network. acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.' author: - first_name: Ksenia full_name: Pougach, Ksenia S last_name: Pougach - first_name: Arnout full_name: Voet, Arnout R last_name: Voet - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Karin full_name: Voordeckers, Karin last_name: Voordeckers - first_name: Joaquin full_name: Christiaens, Joaquin F last_name: Christiaens - first_name: Bianka full_name: Baying, Bianka last_name: Baying - first_name: Vladimı́R full_name: Bénès, Vladimı́r last_name: Bénès - first_name: Ryo full_name: Sakai, Ryo last_name: Sakai - first_name: Jan full_name: Aerts, Jan A last_name: Aerts - first_name: Bo full_name: Zhu, Bo last_name: Zhu - first_name: Patrick full_name: Van Dijck, Patrick last_name: Van Dijck - first_name: Kevin full_name: Verstrepen, Kevin J last_name: Verstrepen citation: ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 2014;5. doi:10.1038/ncomms5868 apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms5868 chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868. ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5. mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications, vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868. short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014). date_created: 2018-12-11T11:48:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:20:01Z day: '01' doi: 10.1038/ncomms5868 extern: 1 intvolume: ' 5' month: '01' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '6790' quality_controlled: 0 status: public title: Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 5 year: '2014' ... --- _id: '863' abstract: - lang: eng text: The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals. acknowledgement: We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22. author: - first_name: Leonid full_name: Moroz, Leonid L last_name: Moroz - first_name: Kevin full_name: Kocot, Kevin M last_name: Kocot - first_name: Mathew full_name: Citarella, Mathew R last_name: Citarella - first_name: Sohn full_name: Dosung, Sohn last_name: Dosung - first_name: Tigran full_name: Norekian, Tigran P last_name: Norekian - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Anastasia full_name: Grigorenko, Anastasia P last_name: Grigorenko - first_name: Christopher full_name: Dailey, Christopher A last_name: Dailey - first_name: Eugene full_name: Berezikov, Eugene last_name: Berezikov - first_name: Katherine full_name: Buckley, Katherine M last_name: Buckley - first_name: Andrey full_name: Ptitsyn, Andrey A last_name: Ptitsyn - first_name: Denis full_name: Reshetov, Denis A last_name: Reshetov - first_name: Krishanu full_name: Mukherjee, Krishanu last_name: Mukherjee - first_name: Tatiana full_name: Moroz, Tatiana P last_name: Moroz - first_name: Yelena full_name: Bobkova, Yelena V last_name: Bobkova - first_name: Fahong full_name: Yu, Fahong last_name: Yu - first_name: Vladimir full_name: Kapitonov, Vladimir V last_name: Kapitonov - first_name: Jerzy full_name: Jurka, Jerzy W last_name: Jurka - first_name: Yuriy full_name: Bobkov, Yuriy V last_name: Bobkov - first_name: Joshua full_name: Swore, Joshua J last_name: Swore - first_name: David full_name: Girardo, David O last_name: Girardo - first_name: Alexander full_name: Fodor, Alexander last_name: Fodor - first_name: Fedor full_name: Gusev, Fedor E last_name: Gusev - first_name: Rachel full_name: Sanford, Rachel S last_name: Sanford - first_name: Rebecca full_name: Bruders, Rebecca last_name: Bruders - first_name: Ellen full_name: Kittler, Ellen L last_name: Kittler - first_name: Claudia full_name: Mills, Claudia E last_name: Mills - first_name: Jonathan full_name: Rast, Jonathan P last_name: Rast - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Victor full_name: Solovyev, Victor last_name: Solovyev - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Billie full_name: Swalla, Billie J last_name: Swalla - first_name: Jonathan full_name: Sweedler, Jonathan V last_name: Sweedler - first_name: Evgeny full_name: Rogaev, Evgeny I last_name: Rogaev - first_name: Kenneth full_name: Halanych, Kenneth M last_name: Halanych - first_name: Andrea full_name: Kohn, Andrea B last_name: Kohn citation: ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400 apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400 chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13400. ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014. ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114. mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:10.1038/nature13400. short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114. date_created: 2018-12-11T11:48:54Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:20:21Z day: '01' doi: 10.1038/nature13400 extern: 1 intvolume: ' 510' issue: '7503' license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '01' page: 109 - 114 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6785' quality_controlled: 0 status: public title: The ctenophore genome and the evolutionary origins of neural systems tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article volume: 510 year: '2014' ... --- _id: '865' abstract: - lang: eng text: Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers. author: - first_name: Alexey full_name: Koval, Alexey V last_name: Koval - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Polina full_name: Shichkova, Polina last_name: Shichkova - first_name: S full_name: Khunderyakova, S last_name: Khunderyakova - first_name: Yury full_name: Markov, Yury last_name: Markov - first_name: J full_name: Panchenko, J last_name: Panchenko - first_name: A full_name: Volodina, A last_name: Volodina - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Katanaev, Vladimir L last_name: Katanaev citation: ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007 apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007 chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014. https://doi.org/10.1016/j.bcp.2013.12.007. ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014. ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578. mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007. short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578. date_created: 2018-12-11T11:48:55Z date_published: 2014-02-15T00:00:00Z date_updated: 2021-01-12T08:20:24Z day: '15' doi: 10.1016/j.bcp.2013.12.007 extern: 1 intvolume: ' 87' issue: '4' month: '02' page: 571 - 578 publication: Biochemical Pharmacology publication_status: published publisher: Elsevier publist_id: '6782' quality_controlled: 0 status: public title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling type: journal_article volume: 87 year: '2014' ... --- _id: '925' abstract: - lang: eng text: The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape. acknowledgement: We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D. article_processing_charge: No author: - first_name: Bo full_name: Dong, Bo last_name: Dong - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Shigeo full_name: Hayashi, Shigeo last_name: Hayashi citation: ama: Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950. doi:10.1016/j.celrep.2014.03.066 apa: Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066 chicago: Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066. ieee: B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” Cell Reports, vol. 7, no. 4. Cell Press, pp. 941–950, 2014. ista: Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950. mla: Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066. short: B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950. date_created: 2018-12-11T11:49:14Z date_published: 2014-05-22T00:00:00Z date_updated: 2021-01-12T08:21:57Z day: '22' doi: 10.1016/j.celrep.2014.03.066 extern: '1' intvolume: ' 7' issue: '4' language: - iso: eng month: '05' oa_version: None page: 941 - 950 publication: Cell Reports publication_status: published publisher: Cell Press publist_id: '6515' status: public title: Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2014' ... --- _id: '927' abstract: - lang: eng text: Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jacques full_name: Prost, Jacques last_name: Prost - first_name: Jean full_name: Joanny, Jean last_name: Joanny citation: ama: Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111 apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111 chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1312076111. ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014. ista: Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32. mla: Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:10.1073/pnas.1312076111. short: E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32. date_created: 2018-12-11T11:49:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:21:58Z day: '01' doi: 10.1073/pnas.1312076111 extern: '1' intvolume: ' 111' issue: '1' language: - iso: eng month: '01' oa_version: None page: 27 - 32 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6517' status: public title: Theory of epithelial sheet morphology in three dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '9519' abstract: - lang: eng text: Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression. article_processing_charge: No article_type: review author: - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014 apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014 chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014. ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326, 2014. ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326. mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:10.1016/j.tplants.2014.01.014. short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326. date_created: 2021-06-07T14:38:09Z date_published: 2014-05-04T00:00:00Z date_updated: 2021-12-14T08:24:48Z day: '04' department: - _id: DaZi doi: 10.1016/j.tplants.2014.01.014 extern: '1' external_id: pmid: - '24618094 ' intvolume: ' 19' issue: '5' language: - iso: eng month: '05' oa_version: None page: 320-326 pmid: 1 publication: Trends in Plant Science publication_identifier: eissn: - 1878-4372 issn: - 1360-1385 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation as a system of plant genomic immunity type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 19 year: '2014' ... --- _id: '96' abstract: - lang: eng text: Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (>1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range. acknowledgement: The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation. article_number: '026801' author: - 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: Micah full_name: Hanson, Micah last_name: Hanson - first_name: Arthur full_name: Gossard, Arthur last_name: Gossard - first_name: Charles full_name: Marcus, Charles last_name: Marcus citation: ama: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 2014;112(2). doi:10.1103/PhysRevLett.112.026801 apa: Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., & Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. American Physiological Society. https://doi.org/10.1103/PhysRevLett.112.026801 chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” APS Physics, Physical Review Letters. American Physiological Society, 2014. https://doi.org/10.1103/PhysRevLett.112.026801. ieee: A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” APS Physics, Physical Review Letters, vol. 112, no. 2. American Physiological Society, 2014. ista: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801. mla: Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” APS Physics, Physical Review Letters, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:10.1103/PhysRevLett.112.026801. short: A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014). date_created: 2018-12-11T11:44:36Z date_published: 2014-01-14T00:00:00Z date_updated: 2021-01-12T08:22:14Z day: '14' doi: 10.1103/PhysRevLett.112.026801 extern: '1' external_id: arxiv: - '1306.2720' intvolume: ' 112' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1306.2720 month: '01' oa: 1 oa_version: Preprint publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physiological Society publist_id: '7958' quality_controlled: '1' status: public title: Coherent operations and screening in multielectron spin qubits type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2014' ... --- _id: '9594' abstract: - lang: eng text: Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture. article_number: P1.45 article_processing_charge: No article_type: original author: - first_name: Catherine full_name: Greenhill, Catherine last_name: Greenhill - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: David full_name: Wind, David last_name: Wind citation: ama: Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752 apa: Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752 chicago: Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752. ieee: C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” The Electronic Journal of Combinatorics, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014. ista: Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45. mla: Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752. short: C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014). date_created: 2021-06-23T06:29:35Z date_published: 2014-02-28T00:00:00Z date_updated: 2023-02-23T14:02:12Z day: '28' doi: 10.37236/3752 extern: '1' external_id: arxiv: - '1309.6710' intvolume: ' 21' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.37236/3752 month: '02' oa: 1 oa_version: Published Version publication: The Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: The Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: On the number of spanning trees in random regular graphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 21 year: '2014' ... --- _id: '9655' abstract: - lang: eng text: Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells. article_processing_charge: No article_type: original author: - first_name: Mario full_name: Perkovic, Mario last_name: Perkovic - first_name: Michael full_name: Kunz, Michael last_name: Kunz - first_name: Ulrike full_name: Endesfelder, Ulrike last_name: Endesfelder - first_name: Stefanie full_name: Bunse, Stefanie last_name: Bunse - first_name: Christoph full_name: Wigge, Christoph last_name: Wigge - first_name: Zhou full_name: Yu, Zhou last_name: Yu - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: Margot P. full_name: Scheffer, Margot P. last_name: Scheffer - first_name: Anja full_name: Seybert, Anja last_name: Seybert - first_name: Sebastian full_name: Malkusch, Sebastian last_name: Malkusch - first_name: Erin M. full_name: Schuman, Erin M. last_name: Schuman - first_name: Mike full_name: Heilemann, Mike last_name: Heilemann - first_name: Achilleas S. full_name: Frangakis, Achilleas S. last_name: Frangakis citation: ama: Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 2014;186(2):205-213. doi:10.1016/j.jsb.2014.03.018 apa: Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018 chicago: Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.jsb.2014.03.018. ieee: M. Perkovic et al., “Correlative light- and electron microscopy with chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier, pp. 205–213, 2014. ista: Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213. mla: Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:10.1016/j.jsb.2014.03.018. short: M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213. date_created: 2021-07-14T09:05:42Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-07-22T08:26:32Z day: '01' ddc: - '570' doi: 10.1016/j.jsb.2014.03.018 extern: '1' external_id: pmid: - '24698954' file: - access_level: open_access checksum: a322991b43cdc5935c99db88d285aa3a content_type: application/pdf creator: asandaue date_created: 2021-07-22T08:06:34Z date_updated: 2021-07-22T08:06:34Z file_id: '9701' file_name: 2014_JournalOfStructuralBiology_Perkovic.pdf file_size: 3454628 relation: main_file success: 1 file_date_updated: 2021-07-22T08:06:34Z has_accepted_license: '1' intvolume: ' 186' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/3.0/ month: '05' oa: 1 oa_version: Published Version page: 205-213 pmid: 1 publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Correlative light- and electron microscopy with chemical tags tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 186 year: '2014' ... --- _id: '9686' abstract: - lang: eng text: It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings. article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: H.S. full_name: Leung, H.S. last_name: Leung - first_name: A.H.W. full_name: Ngan, A.H.W. last_name: Ngan citation: ama: Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 2014;95(16-18):1845-1865. doi:10.1080/14786435.2014.897008 apa: Cheng, B., Leung, H. S., & Ngan, A. H. W. (2014). Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. Taylor & Francis. https://doi.org/10.1080/14786435.2014.897008 chicago: Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical Magazine. Taylor & Francis, 2014. https://doi.org/10.1080/14786435.2014.897008. ieee: B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations – dislocation-density-function dynamics simulations,” Philosophical Magazine, vol. 95, no. 16–18. Taylor & Francis, pp. 1845–1865, 2014. ista: Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865. mla: Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical Magazine, vol. 95, no. 16–18, Taylor & Francis, 2014, pp. 1845–65, doi:10.1080/14786435.2014.897008. short: B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865. date_created: 2021-07-19T09:27:15Z date_published: 2014-06-23T00:00:00Z date_updated: 2023-02-23T14:04:59Z day: '23' doi: 10.1080/14786435.2014.897008 extern: '1' intvolume: ' 95' issue: 16-18 language: - iso: eng month: '06' oa_version: None page: 1845-1865 publication: Philosophical Magazine publication_identifier: eissn: - 1478-6443 issn: - 1478-6435 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: Strength of metals under vibrations – dislocation-density-function dynamics simulations type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 95 year: '2014' ... --- _id: '2083' abstract: - lang: eng text: Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment. acknowledgement: The authors are grateful to the Leverhulme Trust (F/00 215/AW) for funding this work. article_processing_charge: No article_type: original author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Andrew full_name: Morgan, Andrew last_name: Morgan - first_name: Paul full_name: Neve, Paul last_name: Neve - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave citation: ama: Lagator M, Morgan A, Neve P, Colegrave N. Role of sex and migration in adaptation to sink environments. Evolution. 2014;68(8):2296-2305. doi:10.1111/evo.12440 apa: Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Role of sex and migration in adaptation to sink environments. Evolution. Wiley. https://doi.org/10.1111/evo.12440 chicago: Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution. Wiley, 2014. https://doi.org/10.1111/evo.12440. ieee: M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Role of sex and migration in adaptation to sink environments,” Evolution, vol. 68, no. 8. Wiley, pp. 2296–2305, 2014. ista: Lagator M, Morgan A, Neve P, Colegrave N. 2014. Role of sex and migration in adaptation to sink environments. Evolution. 68(8), 2296–2305. mla: Lagator, Mato, et al. “Role of Sex and Migration in Adaptation to Sink Environments.” Evolution, vol. 68, no. 8, Wiley, 2014, pp. 2296–305, doi:10.1111/evo.12440. short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, Evolution 68 (2014) 2296–2305. date_created: 2018-12-11T11:55:36Z date_published: 2014-04-25T00:00:00Z date_updated: 2023-02-23T14:06:51Z day: '25' ddc: - '570' department: - _id: CaGu doi: 10.1111/evo.12440 file: - access_level: open_access checksum: 8d459b07e4a11bb5fde92d969184fe48 content_type: application/pdf creator: dernst date_created: 2020-05-14T16:40:31Z date_updated: 2020-07-14T12:45:28Z file_id: '7845' file_name: 2014_Evolution_Lagator.pdf file_size: 467254 relation: main_file file_date_updated: 2020-07-14T12:45:28Z has_accepted_license: '1' intvolume: ' 68' issue: '8' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 2296 - 2305 publication: Evolution publication_status: published publisher: Wiley publist_id: '4954' quality_controlled: '1' related_material: record: - id: '9747' relation: research_data status: public scopus_import: 1 status: public title: Role of sex and migration in adaptation to sink environments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2014' ... --- _id: '9747' abstract: - lang: eng text: Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment. article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Andrew full_name: Morgan, Andrew last_name: Morgan - first_name: Paul full_name: Neve, Paul last_name: Neve - first_name: Nick full_name: Colegrave, Nick last_name: Colegrave citation: ama: 'Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:10.5061/dryad.s42n1' apa: 'Lagator, M., Morgan, A., Neve, P., & Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. https://doi.org/10.5061/dryad.s42n1' chicago: 'Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. https://doi.org/10.5061/dryad.s42n1.' ieee: 'M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.' ista: 'Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, 10.5061/dryad.s42n1.' mla: 'Lagator, Mato, et al. Data from: Role of Sex and Migration in Adaptation to Sink Environments. Dryad, 2014, doi:10.5061/dryad.s42n1.' short: M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014). date_created: 2021-07-28T15:32:55Z date_published: 2014-04-17T00:00:00Z date_updated: 2023-02-23T10:27:31Z day: '17' department: - _id: CaGu doi: 10.5061/dryad.s42n1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.s42n1 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2083' relation: used_in_publication status: public status: public title: 'Data from: Role of sex and migration in adaptation to sink environments' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '977' abstract: - lang: eng text: We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems. acknowledgement: |- We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario. M. S., M. K., and S. G. contributed equally to this work. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Michael full_name: Knap, Michael J last_name: Knap - first_name: Sarang full_name: Gopalakrishnan, Sarang last_name: Gopalakrishnan - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Norman full_name: Yao, Norman Y last_name: Yao - first_name: Chris full_name: Laumann, Chris R last_name: Laumann - first_name: Dmitry full_name: Abanin, Dmitry A last_name: Abanin - first_name: Mikhail full_name: Lukin, Mikhail D last_name: Lukin - first_name: Eugene full_name: Demler, Eugene A last_name: Demler citation: ama: Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body localization. Physical Review Letters. 2014;113(14). doi:10.1103/PhysRevLett.113.147204 apa: Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C., … Demler, E. (2014). Interferometric probes of many-body localization. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.147204 chicago: Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric Probes of Many-Body Localization.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.147204. ieee: M. Serbyn et al., “Interferometric probes of many-body localization,” Physical Review Letters, vol. 113, no. 14. American Physical Society, 2014. ista: Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin M, Demler E. 2014. Interferometric probes of many-body localization. Physical Review Letters. 113(14). mla: Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.” Physical Review Letters, vol. 113, no. 14, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.147204. short: M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin, M. Lukin, E. Demler, Physical Review Letters 113 (2014). date_created: 2018-12-11T11:49:30Z date_published: 2014-10-03T00:00:00Z date_updated: 2021-01-12T08:22:22Z day: '03' doi: 10.1103/PhysRevLett.113.147204 extern: 1 intvolume: ' 113' issue: '14' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.0693 month: '10' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6421' quality_controlled: 0 status: public title: Interferometric probes of many-body localization type: journal_article volume: 113 year: '2014' ... --- _id: '980' abstract: - lang: eng text: Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization. acknowledgement: Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. We acknowledge support by NSERC Discovery Grant (D.A.). author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Dmitry full_name: Abanin, Dmitry A last_name: Abanin citation: ama: Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 2014;90(17). doi:10.1103/PhysRevB.90.174302 apa: Serbyn, M., Papić, Z., & Abanin, D. (2014). Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.90.174302 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2014. https://doi.org/10.1103/PhysRevB.90.174302. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized phase,” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17. American Physical Society, 2014. ista: Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 90(17). mla: Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.” Physical Review B - Condensed Matter and Materials Physics, vol. 90, no. 17, American Physical Society, 2014, doi:10.1103/PhysRevB.90.174302. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 90 (2014). date_created: 2018-12-11T11:49:31Z date_published: 2014-11-06T00:00:00Z date_updated: 2021-01-12T08:22:24Z day: '06' doi: 10.1103/PhysRevB.90.174302 extern: 1 intvolume: ' 90' issue: '17' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.4105 month: '11' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6420' quality_controlled: 0 status: public title: Quantum quenches in the many-body localized phase type: journal_article volume: 90 year: '2014' ... --- _id: '98' abstract: - lang: eng text: Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing. acknowledgement: Funding from the Department of Energy, Office of Science & SCGF, the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation is acknowledged. author: - 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: Thorvald full_name: Larsen, Thorvald last_name: Larsen - first_name: Jun full_name: Yao, Jun last_name: Yao - first_name: Hao full_name: Yan, Hao last_name: Yan - first_name: Charles full_name: Lieber, Charles last_name: Lieber - first_name: Charles full_name: Marcus, Charles last_name: Marcus - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth citation: ama: Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 2014;14(6):3582-3586. doi:10.1021/nl501242b apa: Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C., & Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. American Chemical Society. https://doi.org/10.1021/nl501242b chicago: Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber, Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” Nano Letters. American Chemical Society, 2014. https://doi.org/10.1021/nl501242b. ieee: A. P. Higginbotham et al., “Hole spin coherence in a Ge/Si heterostructure nanowire,” Nano Letters, vol. 14, no. 6. American Chemical Society, pp. 3582–3586, 2014. ista: Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6), 3582–3586. mla: Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” Nano Letters, vol. 14, no. 6, American Chemical Society, 2014, pp. 3582–86, doi:10.1021/nl501242b. short: A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth, Nano Letters 14 (2014) 3582–3586. date_created: 2018-12-11T11:44:37Z date_published: 2014-05-05T00:00:00Z date_updated: 2021-01-12T08:22:24Z day: '05' doi: 10.1021/nl501242b extern: '1' external_id: arxiv: - '1403.2093' intvolume: ' 14' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.2093 month: '05' oa: 1 oa_version: Preprint page: 3582 - 3586 publication: Nano Letters publication_status: published publisher: American Chemical Society publist_id: '7956' quality_controlled: '1' status: public title: Hole spin coherence in a Ge/Si heterostructure nanowire type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '2086' abstract: - lang: eng text: Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed. acknowledgement: This study was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative (grant numbers BB/I00097/1 and BB/I000100/1). Rothamsted Research is a national institute of bioscience strategically funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC). article_number: e103989 author: - first_name: Stephan full_name: Wolf, Stephan last_name: Wolf - first_name: Dino full_name: Mcmahon, Dino last_name: Mcmahon - first_name: Ka full_name: Lim, Ka last_name: Lim - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Suzanne full_name: Clark, Suzanne last_name: Clark - first_name: Robert full_name: Paxton, Robert last_name: Paxton - first_name: Juliet full_name: Osborne, Juliet last_name: Osborne citation: ama: 'Wolf S, Mcmahon D, Lim K, et al. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 2014;9(8). doi:10.1371/journal.pone.0103989' apa: 'Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., & Osborne, J. (2014). So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0103989' chicago: 'Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0103989.' ieee: 'S. Wolf et al., “So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees,” PLoS One, vol. 9, no. 8. Public Library of Science, 2014.' ista: 'Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees. PLoS One. 9(8), e103989.' mla: 'Wolf, Stephan, et al. “So near and yet so Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees.” PLoS One, vol. 9, no. 8, e103989, Public Library of Science, 2014, doi:10.1371/journal.pone.0103989.' short: S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, PLoS One 9 (2014). date_created: 2018-12-11T11:55:37Z date_published: 2014-08-06T00:00:00Z date_updated: 2023-02-23T14:11:56Z day: '06' ddc: - '570' department: - _id: SyCr doi: 10.1371/journal.pone.0103989 file: - access_level: open_access checksum: 2fc62c6739eada4bddf026afbae669db content_type: application/pdf creator: system date_created: 2018-12-12T10:13:55Z date_updated: 2020-07-14T12:45:28Z file_id: '5042' file_name: IST-2016-437-v1+1_journal.pone.0103989.pdf file_size: 1013386 relation: main_file file_date_updated: 2020-07-14T12:45:28Z has_accepted_license: '1' intvolume: ' 9' issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4949' pubrep_id: '437' quality_controlled: '1' related_material: record: - id: '9888' relation: research_data status: public scopus_import: 1 status: public title: 'So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees' 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ...