--- _id: '352' abstract: - lang: eng text: The presence of organic ligands on the surface of colloidal nanoparticles strongly limits their performance in technological applications where charge carrier transfer/transport plays an important role. We use metal salts, matched with the nanoparticle composition, to eliminate the surface organic ligands without introducing extrinsic impurities in the final nanomaterial. The potential of the simple, general and scalable processes presented here is demonstrated by characterizing the thermoelectric properties of nanostructured Ag2Te produced by the bottom up assembly of Ag2Te nanocrystals. A 6-fold increase of the thermoelectric figure of merit of Ag2Te was obtained when organic ligands were displaced by AgNO3. The same procedure can enhance the performance of nanocrystals and nanocrystal-based devices in a broad range of applications, from photovoltaics and thermoelectrics to catalysis. article_processing_charge: No article_type: original author: - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Oscar full_name: Durá, Oscar last_name: Durá - first_name: Marco full_name: López De La Torre, Marco last_name: López De La Torre - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Cadavid D, Ibáñez M, Shavel A, Durá O, López De La Torre M, Cabot A. Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials Chemistry A. 2013;1(15):4864-4870. doi:10.1039/C3TA01455J' apa: 'Cadavid, D., Ibáñez, M., Shavel, A., Durá, O., López De La Torre, M., & Cabot, A. (2013). Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials Chemistry A. Royal Society of Chemistry. https://doi.org/10.1039/C3TA01455J' chicago: 'Cadavid, Doris, Maria Ibáñez, Alexey Shavel, Oscar Durá, Marco López De La Torre, and Andreu Cabot. “Organic Ligand Displacement by Metal Salts to Enhance Nanoparticle Functionality: Thermoelectric Properties of Ag Inf 2 Inf Te.” Journal of Materials Chemistry A. Royal Society of Chemistry, 2013. https://doi.org/10.1039/C3TA01455J.' ieee: 'D. Cadavid, M. Ibáñez, A. Shavel, O. Durá, M. López De La Torre, and A. Cabot, “Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te,” Journal of Materials Chemistry A, vol. 1, no. 15. Royal Society of Chemistry, pp. 4864–4870, 2013.' ista: 'Cadavid D, Ibáñez M, Shavel A, Durá O, López De La Torre M, Cabot A. 2013. Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te. Journal of Materials Chemistry A. 1(15), 4864–4870.' mla: 'Cadavid, Doris, et al. “Organic Ligand Displacement by Metal Salts to Enhance Nanoparticle Functionality: Thermoelectric Properties of Ag Inf 2 Inf Te.” Journal of Materials Chemistry A, vol. 1, no. 15, Royal Society of Chemistry, 2013, pp. 4864–70, doi:10.1039/C3TA01455J.' short: D. Cadavid, M. Ibáñez, A. Shavel, O. Durá, M. López De La Torre, A. Cabot, Journal of Materials Chemistry A 1 (2013) 4864–4870. date_created: 2018-12-11T11:45:58Z date_published: 2013-02-13T00:00:00Z date_updated: 2021-01-12T07:44:02Z day: '13' doi: 10.1039/C3TA01455J extern: '1' intvolume: ' 1' issue: '15' language: - iso: eng month: '02' oa_version: None page: 4864 - 4870 publication: Journal of Materials Chemistry A publication_status: published publisher: Royal Society of Chemistry publist_id: '7481' quality_controlled: '1' status: public title: 'Organic ligand displacement by metal salts to enhance nanoparticle functionality: Thermoelectric properties of Ag inf 2 inf Te' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '378' abstract: - lang: eng text: Until recently, to prepare nanocrystals of a new material, scientists searched their shelves for the appropriate molecular precursors, surfactants, and solvents. They then optimized the reaction conditions for the atoms to self-assemble into monodisperse nanocrystals (1). This approach is being replaced by a simpler strategy, in which preformed nanocrystals serve as templates to produce nanoparticles with a different composition through chemical transformation. On page 964 of this issue, Oh et al. (2) report a powerful mechanism that allows the composition of oxide nanoparticles to be transformed in solution and at low temperatures. article_processing_charge: No author: - 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: Ibáñez M, Cabot A. All change for nanocrystals. Science. 2013;340(6135):935-936. doi:10.1126/science.1239221 apa: Ibáñez, M., & Cabot, A. (2013). All change for nanocrystals. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1239221 chicago: Ibáñez, Maria, and Andreu Cabot. “All Change for Nanocrystals.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239221. ieee: M. Ibáñez and A. Cabot, “All change for nanocrystals,” Science, vol. 340, no. 6135. American Association for the Advancement of Science, pp. 935–936, 2013. ista: Ibáñez M, Cabot A. 2013. All change for nanocrystals. Science. 340(6135), 935–936. mla: Ibáñez, Maria, and Andreu Cabot. “All Change for Nanocrystals.” Science, vol. 340, no. 6135, American Association for the Advancement of Science, 2013, pp. 935–36, doi:10.1126/science.1239221. short: M. Ibáñez, A. Cabot, Science 340 (2013) 935–936. date_created: 2018-12-11T11:46:08Z date_published: 2013-05-24T00:00:00Z date_updated: 2021-01-12T07:52:09Z day: '24' doi: 10.1126/science.1239221 extern: '1' intvolume: ' 340' issue: '6135' language: - iso: eng month: '05' oa_version: None page: 935 - 936 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '7451' status: public title: All change for nanocrystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 340 year: '2013' ... --- _id: '3261' abstract: - lang: eng text: Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network. author: - first_name: Julien full_name: Dubuis, Julien last_name: Dubuis - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Eric full_name: Wieschaus, Eric last_name: Wieschaus - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. PNAS. 2013;110(41):16301-16308. doi:10.1073/pnas.1315642110 apa: Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., & Bialek, W. (2013). Positional information, in bits. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315642110 chicago: Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1315642110. ieee: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013. ista: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308. mla: Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110. short: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308. date_created: 2018-12-11T12:02:19Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T07:42:13Z day: '08' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.1315642110 external_id: pmid: - '24089448' file: - access_level: open_access checksum: ecd859fe52a562193027d428b5524a8d content_type: application/pdf creator: dernst date_created: 2019-01-22T13:53:23Z date_updated: 2020-07-14T12:46:06Z file_id: '5873' file_name: 2013_PNAS_Dubuis.pdf file_size: 1670548 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 110' issue: '41' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 16301 - 16308 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3387' quality_controlled: '1' scopus_import: 1 status: public title: Positional information, in bits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '331' abstract: - lang: eng text: We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents. article_processing_charge: No article_type: original author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Pilar full_name: Rivera Gil, Pilar last_name: Rivera Gil - first_name: Beatriz full_name: Pelaz, Beatriz last_name: Pelaz - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Ramon full_name: Alvarez Puebla, Ramon last_name: Alvarez Puebla - first_name: Wolfgang full_name: Parak, Wolfgang last_name: Parak - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 2013;135(19):7098-7101. doi:10.1021/ja401428e' apa: 'Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., … Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja401428e' chicago: 'Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez, Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society. ACS, 2013. https://doi.org/10.1021/ja401428e.' ieee: 'W. Li et al., “CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents,” Journal of the American Chemical Society, vol. 135, no. 19. ACS, pp. 7098–7101, 2013.' ista: 'Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 135(19), 7098–7101.' mla: 'Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society, vol. 135, no. 19, ACS, 2013, pp. 7098–101, doi:10.1021/ja401428e.' short: W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel, R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 7098–7101. date_created: 2018-12-11T11:45:51Z date_published: 2013-04-30T00:00:00Z date_updated: 2021-01-12T07:42:33Z day: '30' doi: 10.1021/ja401428e extern: '1' intvolume: ' 135' issue: '19' language: - iso: eng month: '04' oa_version: None page: 7098 - 7101 publication: Journal of the American Chemical Society publication_status: published publisher: ACS publist_id: '7521' quality_controlled: '1' status: public title: 'CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '3321' author: - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H, eds. Encyclopedia of Systems Biology. Vol 3. Springer; 2013:1069-1069. doi:10.1007/978-1-4419-9863-7_604' apa: Quadrianto, N., & Lampert, C. (2013). Kernel based learning. In W. Dubitzky, O. Wolkenhauer, K. Cho, & H. Yokota (Eds.), Encyclopedia of Systems Biology (Vol. 3, pp. 1069–1069). Springer. https://doi.org/10.1007/978-1-4419-9863-7_604 chicago: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In Encyclopedia of Systems Biology, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho, and Hiroki Yokota, 3:1069–1069. Springer, 2013. https://doi.org/10.1007/978-1-4419-9863-7_604. ieee: N. Quadrianto and C. Lampert, “Kernel based learning,” in Encyclopedia of Systems Biology, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Eds. Springer, 2013, pp. 1069–1069. ista: 'Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of Systems Biology. vol. 3, 1069–1069.' mla: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” Encyclopedia of Systems Biology, edited by Werner Dubitzky et al., vol. 3, Springer, 2013, pp. 1069–1069, doi:10.1007/978-1-4419-9863-7_604. short: N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069. date_created: 2018-12-11T12:02:39Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T07:42:38Z day: '01' department: - _id: ChLa doi: 10.1007/978-1-4419-9863-7_604 editor: - first_name: Werner full_name: Dubitzky, Werner last_name: Dubitzky - first_name: Olaf full_name: Wolkenhauer, Olaf last_name: Wolkenhauer - first_name: Kwang full_name: Cho, Kwang last_name: Cho - first_name: Hiroki full_name: Yokota, Hiroki last_name: Yokota intvolume: ' 3' language: - iso: eng month: '01' oa_version: None page: 1069 - 1069 publication: Encyclopedia of Systems Biology publication_status: published publisher: Springer publist_id: '3314' quality_controlled: '1' status: public title: Kernel based learning type: encyclopedia_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2831' abstract: - lang: eng text: 'We consider Markov decision processes (MDPs) with Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning states from where the objective can be ensured with probability 1. Our contributions are as follows: First, we present the first subquadratic symbolic algorithm to compute the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes O(n · √ m) symbolic steps as compared to the previous known algorithm that takes O(n 2) symbolic steps, where n is the number of states and m is the number of edges of the MDP. In practice MDPs have constant out-degree, and then our symbolic algorithm takes O(n · √ n) symbolic steps, as compared to the previous known O(n 2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose algorithm, with the following two properties: (a) the algorithm iteratively computes subsets of the almost-sure winning set and its complement, as compared to all previous algorithms that discover the almost-sure winning set upon termination; and (b) requires O(n · √ K) symbolic steps, where K is the maximal number of edges of strongly connected components (scc''s) of the MDP. The win-lose algorithm requires symbolic computation of scc''s. Third, we improve the algorithm for symbolic scc computation; the previous known algorithm takes linear symbolic steps, and our new algorithm improves the constants associated with the linear number of steps. In the worst case the previous known algorithm takes 5×n symbolic steps, whereas our new algorithm takes 4×n symbolic steps.' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Manas full_name: Joglekar, Manas last_name: Joglekar - first_name: Nisarg full_name: Shah, Nisarg last_name: Shah citation: ama: Chatterjee K, Henzinger MH, Joglekar M, Shah N. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. Formal Methods in System Design. 2013;42(3):301-327. doi:10.1007/s10703-012-0180-2 apa: Chatterjee, K., Henzinger, M. H., Joglekar, M., & Shah, N. (2013). Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0180-2 chicago: Chatterjee, Krishnendu, Monika H Henzinger, Manas Joglekar, and Nisarg Shah. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” Formal Methods in System Design. Springer, 2013. https://doi.org/10.1007/s10703-012-0180-2. ieee: K. Chatterjee, M. H. Henzinger, M. Joglekar, and N. Shah, “Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives,” Formal Methods in System Design, vol. 42, no. 3. Springer, pp. 301–327, 2013. ista: Chatterjee K, Henzinger MH, Joglekar M, Shah N. 2013. Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives. Formal Methods in System Design. 42(3), 301–327. mla: Chatterjee, Krishnendu, et al. “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with Büchi Objectives.” Formal Methods in System Design, vol. 42, no. 3, Springer, 2013, pp. 301–27, doi:10.1007/s10703-012-0180-2. short: K. Chatterjee, M.H. Henzinger, M. Joglekar, N. Shah, Formal Methods in System Design 42 (2013) 301–327. date_created: 2018-12-11T11:59:49Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-02-23T11:23:04Z day: '01' department: - _id: KrCh doi: 10.1007/s10703-012-0180-2 ec_funded: 1 external_id: arxiv: - '1104.3348' intvolume: ' 42' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.3348 month: '06' oa: 1 oa_version: Preprint page: 301 - 327 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: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '3968' quality_controlled: '1' related_material: record: - id: '3342' relation: earlier_version status: public scopus_import: '1' status: public title: Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 42 year: '2013' ... --- _id: '342' abstract: - lang: eng text: Morphology is a key parameter in the design of novel nanocrystals and nanomaterials with controlled functional properties. Here, we demonstrate the potential of foreign metal ions to tune the morphology of colloidal semiconductor nanoparticles. We illustrate the underlying mechanism by preparing copper selenide nanocubes in the presence of Al ions. We further characterize the plasmonic properties of the obtained nanocrystals and demonstrate their potential as a platform to produce cubic nanoparticles with different composition by cation exchange. © 2013 American Chemical Society. acknowledgement: The research was supported by the European Regional Development Funds. M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge MAT2010-15138. article_processing_charge: No article_type: original author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Zamani R, Ibáñez M, et al. Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. Journal of the American Chemical Society. 2013;135(12):4664-4667. doi:10.1021/ja400472m' apa: 'Li, W., Zamani, R., Ibáñez, M., Cadavid, D., Shavel, A., Morante, J., … Cabot, A. (2013). Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja400472m' chicago: 'Li, Wenhua, Reza Zamani, Maria Ibáñez, Doris Cadavid, Alexey Shavel, Joan Morante, Jordi Arbiol, and Andreu Cabot. “Metal Ions to Control the Morphology of Semiconductor Nanoparticles: Copper Selenide Nanocubes.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja400472m.' ieee: 'W. Li et al., “Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes,” Journal of the American Chemical Society, vol. 135, no. 12. American Chemical Society, pp. 4664–4667, 2013.' ista: 'Li W, Zamani R, Ibáñez M, Cadavid D, Shavel A, Morante J, Arbiol J, Cabot A. 2013. Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. Journal of the American Chemical Society. 135(12), 4664–4667.' mla: 'Li, Wenhua, et al. “Metal Ions to Control the Morphology of Semiconductor Nanoparticles: Copper Selenide Nanocubes.” Journal of the American Chemical Society, vol. 135, no. 12, American Chemical Society, 2013, pp. 4664–67, doi:10.1021/ja400472m.' short: W. Li, R. Zamani, M. Ibáñez, D. Cadavid, A. Shavel, J. Morante, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 4664–4667. date_created: 2018-12-11T11:45:55Z date_published: 2013-03-07T00:00:00Z date_updated: 2021-01-12T07:43:21Z day: '07' doi: 10.1021/ja400472m extern: '1' intvolume: ' 135' issue: '12' language: - iso: eng month: '03' oa_version: None page: 4664 - 4667 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7482' quality_controlled: '1' status: public title: 'Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '343' abstract: - lang: eng text: The bottom-up assembly of nanocrystals provides access to a three-dimensional composition control at the nanoscale not attainable by any other technology. In particular, colloidal nanoheterostructures, with intrinsic multiphase organization, are especially appealing building blocks for the bottom-up production of nanocomposites. In the present work, we use PbTe-PbS as the model material system and thermoelectricity as the paradigmatic application to investigate the potential of the bottom-up assembly of core-shell nanoparticles to produce functional nanocomposites. With this goal in mind, a rapid, high-yield and scalable colloidal synthetic route to prepare grams of PbTe@PbS core-shell nanoparticles with unprecedented narrow size distributions and exceptional composition control is detailed. PbTe@PbS nanoparticles were used as building blocks for the bottom-up production of PbTe-PbS nanocomposites with tuned composition. In such PbTe-PbS nanocomposites, synergistic nanocrystal doping effects result in up to 10-fold higher electrical conductivities than in pure PbTe and PbS nanomaterials. At the same time, the acoustic impedance mismatch between PbTe and PbS phases and a partial phase alloying provide PbTe-PbS nanocomposites with strongly reduced thermal conductivities. As a result, record thermoelectric figures of merit (ZT) of ∼1.1 were obtained from undoped PbTe and PbS phases at 710 K. These high ZT values prove the potential of the proposed processes to produce efficient functional nanomaterials with programmable properties. © 2013 American Chemical Society. acknowledgement: "The research was supported by the European Regional Development Funds (ERDF, “FEDER Programa Competitivitat de Catalunya 2007-2013”) and the Spanish MICINN Projects MAT2008-05779, MAT2010-15138, CSD2009-00050, and CSD2009-00013. M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE.\r\n\r\nThe authors declare no competing financial interest." article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Stéphane full_name: Gorsse, Stéphane last_name: Gorsse - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Silvia full_name: Ortega, Silvia last_name: Ortega - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Ibáñez M, Zamani R, Gorsse S, et al. Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties. ACS Nano. 2013;7(3):2573-2586. doi:10.1021/nn305971v' apa: 'Ibáñez, M., Zamani, R., Gorsse, S., Fan, J., Ortega, S., Cadavid, D., … Cabot, A. (2013). Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn305971v' chicago: 'Ibáñez, Maria, Reza Zamani, Stéphane Gorsse, Jiandong Fan, Silvia Ortega, Doris Cadavid, Joan Morante, Jordi Arbiol, and Andreu Cabot. “Core Shell Nanoparticles as Building Blocks for the Bottom-up Production of Functional Nanocomposites: PbTe PbS Thermoelectric Properties.” ACS Nano. American Chemical Society, 2013. https://doi.org/10.1021/nn305971v.' ieee: 'M. Ibáñez et al., “Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties,” ACS Nano, vol. 7, no. 3. American Chemical Society, pp. 2573–2586, 2013.' ista: 'Ibáñez M, Zamani R, Gorsse S, Fan J, Ortega S, Cadavid D, Morante J, Arbiol J, Cabot A. 2013. Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties. ACS Nano. 7(3), 2573–2586.' mla: 'Ibáñez, Maria, et al. “Core Shell Nanoparticles as Building Blocks for the Bottom-up Production of Functional Nanocomposites: PbTe PbS Thermoelectric Properties.” ACS Nano, vol. 7, no. 3, American Chemical Society, 2013, pp. 2573–86, doi:10.1021/nn305971v.' short: M. Ibáñez, R. Zamani, S. Gorsse, J. Fan, S. Ortega, D. Cadavid, J. Morante, J. Arbiol, A. Cabot, ACS Nano 7 (2013) 2573–2586. date_created: 2018-12-11T11:45:55Z date_published: 2013-02-28T00:00:00Z date_updated: 2021-01-12T07:43:25Z day: '28' doi: 10.1021/nn305971v extern: '1' intvolume: ' 7' issue: '3' language: - iso: eng month: '02' oa_version: None page: 2573 - 2586 publication: ACS Nano publication_status: published publisher: American Chemical Society publist_id: '7483' quality_controlled: '1' status: public title: 'Core shell nanoparticles as building blocks for the bottom-up production of functional nanocomposites: PbTe PbS thermoelectric properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2013' ... --- _id: '351' abstract: - lang: eng text: 'A multistrategy approach to overcome the main challenges of nanoparticle-based solution-processed Cu2ZnSnSe4 thin film solar cells is presented. We developed an efficient ligand exchange strategy, using an antimony salt, to displace organic ligands from the surface of Cu 2ZnSnS4 nanoparticles. An automated pulsed spray-deposition system was used to deposit the nanoparticles into homogeneous and crack-free films with controlled thickness. After annealing the film in a Se-rich atmosphere, carbon-free and crystalline Cu2ZnSnSe4 absorber layers were obtained. Not only was crystallization promoted by the complete removal of organics, but also Sb itself played a critical role. The Sb-assisted crystal growth is associated with the formation of a Sb-based compound at the grain boundaries, which locally reduces the melting point, thus promoting the film diffusion-limited crystallization. ' acknowledgement: This work was supported by the European Regional Development Funds and the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486). E.S. thanks the Spanish government for the “Ramon y Cajal” fellowship (RYC-2011-09212). article_processing_charge: No article_type: original author: - first_name: Alex full_name: Carrete, Alex last_name: Carrete - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Xavier full_name: Fontané, Xavier last_name: Fontané - first_name: Joana full_name: Montserrat, Joana last_name: Montserrat - first_name: Jiandong full_name: Fan, Jiandong last_name: Fan - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Edgardo full_name: Saucedo, Edgardo last_name: Saucedo - first_name: Alejandro full_name: Pérez Rodríguez, Alejandro last_name: Pérez Rodríguez - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Carrete A, Shavel A, Fontané X, et al. Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical Society. 2013;135(43):15982-15985. doi:10.1021/ja4068639 apa: Carrete, A., Shavel, A., Fontané, X., Montserrat, J., Fan, J., Ibáñez, M., … Cabot, A. (2013). Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja4068639 chicago: Carrete, Alex, Alexey Shavel, Xavier Fontané, Joana Montserrat, Jiandong Fan, Maria Ibáñez, Edgardo Saucedo, Alejandro Pérez Rodríguez, and Andreu Cabot. “Antimony-Based Ligand Exchange to Promote Crystallization in Spray-Deposited Cu2ZnSnSe4 Solar Cells.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja4068639. ieee: A. Carrete et al., “Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells,” Journal of the American Chemical Society, vol. 135, no. 43. American Chemical Society, pp. 15982–15985, 2013. ista: Carrete A, Shavel A, Fontané X, Montserrat J, Fan J, Ibáñez M, Saucedo E, Pérez Rodríguez A, Cabot A. 2013. Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells. Journal of the American Chemical Society. 135(43), 15982–15985. mla: Carrete, Alex, et al. “Antimony-Based Ligand Exchange to Promote Crystallization in Spray-Deposited Cu2ZnSnSe4 Solar Cells.” Journal of the American Chemical Society, vol. 135, no. 43, American Chemical Society, 2013, pp. 15982–85, doi:10.1021/ja4068639. short: A. Carrete, A. Shavel, X. Fontané, J. Montserrat, J. Fan, M. Ibáñez, E. Saucedo, A. Pérez Rodríguez, A. Cabot, Journal of the American Chemical Society 135 (2013) 15982–15985. date_created: 2018-12-11T11:45:58Z date_published: 2013-10-30T00:00:00Z date_updated: 2021-01-12T07:43:57Z day: '30' doi: 10.1021/ja4068639 extern: '1' intvolume: ' 135' issue: '43' language: - iso: eng month: '10' oa_version: None page: 15982 - 15985 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7479' quality_controlled: '1' status: public title: Antimony-based ligand exchange to promote crystallization in spray-deposited Cu2ZnSnSe4 solar cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '353' abstract: - lang: eng text: We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents. acknowledgement: This research was supported by the European Regional Development Funds. J.A. and R.Z. acknowledge MAT2010-15138. Part of this work was supported by HFSP grant RGP0052/2012 to W.J.P. article_processing_charge: No article_type: original author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Pilar full_name: Rivera Gil, Pilar last_name: Rivera Gil - first_name: Beatriz full_name: Pelaz, Beatriz last_name: Pelaz - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Ramon full_name: Alvarez Puebla, Ramon last_name: Alvarez Puebla - first_name: Wolfgang full_name: Parak, Wolfgang last_name: Parak - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 2013;135(19):7098-7101. doi:10.1021/ja401428e' apa: 'Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., … Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja401428e' chicago: 'Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez, Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja401428e.' ieee: 'W. Li et al., “CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents,” Journal of the American Chemical Society, vol. 135, no. 19. American Chemical Society, pp. 7098–7101, 2013.' ista: 'Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 135(19), 7098–7101.' mla: 'Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” Journal of the American Chemical Society, vol. 135, no. 19, American Chemical Society, 2013, pp. 7098–101, doi:10.1021/ja401428e.' short: W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel, R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 7098–7101. date_created: 2018-12-11T11:45:59Z date_published: 2013-04-30T00:00:00Z date_updated: 2021-01-12T07:44:06Z day: '30' doi: 10.1021/ja401428e extern: '1' intvolume: ' 135' issue: '19' language: - iso: eng month: '04' oa_version: None page: 7098 - 7101 publication: Journal of the American Chemical Society publication_status: published publisher: American Chemical Society publist_id: '7480' quality_controlled: '1' status: public title: 'CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2013' ... --- _id: '376' abstract: - lang: eng text: The compositional versatility of I2–II–IV–VI4 tetrahedrally-coordinated compounds allows for accommodating their functional properties to numerous technological applications. Among them, Cu2ZnSnSe4 is an emerging photovoltaic material and Cu2CdSnSe4 displays excellent thermoelectric properties. The third compound of this family, Cu2HgSnSe4, remains relatively unexplored. Herein, a synthetic route to produce Cu2HgSnSe4 nanoparticles with narrow size distribution and controlled composition is presented. Cu2HgSnSe4 nanoparticles were subsequently used as building blocks to produce bulk nanocrystalline materials, whose thermoelectric properties were analyzed. A very preliminary adjustment of the material composition yielded Seebeck coefficients up to 160 μV K−1, electrical conductivities close to 104 S m−1 and thermal conductivities down to 0.5 W m−1 K−1. author: - first_name: Wenhua full_name: Li, Wenhua last_name: Li - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Reza full_name: Zamani, Reza last_name: Zamani - first_name: Nuria full_name: García Castelló, Nuria last_name: García Castelló - first_name: Grosse full_name: Stéphane, Grosse last_name: Stéphane - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Joan full_name: Prades, Joan last_name: Prades - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Li W, Ibáñez M, Zamani R, et al. Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties. CrystEngComm. 2013;44:8966-8971. doi:10.1039/C3CE41583J' apa: 'Li, W., Ibáñez, M., Zamani, R., García Castelló, N., Stéphane, G., Cadavid, D., … Cabot, A. (2013). Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties. CrystEngComm. Royal Society of Chemistry. https://doi.org/10.1039/C3CE41583J' chicago: 'Li, Wenhua, Maria Ibáñez, Reza Zamani, Nuria García Castelló, Grosse Stéphane, Doris Cadavid, Joan Prades, Jordi Arbiol, and Andreu Cabot. “Cu2HgSnSe4 Nanoparticles: Synthesis and Thermoelectric Properties.” CrystEngComm. Royal Society of Chemistry, 2013. https://doi.org/10.1039/C3CE41583J.' ieee: 'W. Li et al., “Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties,” CrystEngComm, vol. 44. Royal Society of Chemistry, pp. 8966–8971, 2013.' ista: 'Li W, Ibáñez M, Zamani R, García Castelló N, Stéphane G, Cadavid D, Prades J, Arbiol J, Cabot A. 2013. Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties. CrystEngComm. 44, 8966–8971.' mla: 'Li, Wenhua, et al. “Cu2HgSnSe4 Nanoparticles: Synthesis and Thermoelectric Properties.” CrystEngComm, vol. 44, Royal Society of Chemistry, 2013, pp. 8966–71, doi:10.1039/C3CE41583J.' short: W. Li, M. Ibáñez, R. Zamani, N. García Castelló, G. Stéphane, D. Cadavid, J. Prades, J. Arbiol, A. Cabot, CrystEngComm 44 (2013) 8966–8971. date_created: 2018-12-11T11:46:07Z date_published: 2013-09-23T00:00:00Z date_updated: 2021-01-12T07:52:00Z day: '23' doi: 10.1039/C3CE41583J extern: '1' intvolume: ' 44' language: - iso: eng month: '09' oa_version: None page: 8966 - 8971 publication: CrystEngComm publication_status: published publisher: Royal Society of Chemistry publist_id: '7453' quality_controlled: '1' status: public title: 'Cu2HgSnSe4 nanoparticles: synthesis and thermoelectric properties' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2013' ... --- _id: '450' abstract: - lang: eng text: Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations. article_number: '2058' author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: David full_name: Rowell, David last_name: Rowell - first_name: Andrew full_name: Young, Andrew last_name: Young citation: ama: Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1750). doi:10.1098/rspb.2012.2058 apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058 chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058. ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750. Royal Society, The, 2013. ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058. mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1750, 2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058. short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013). date_created: 2018-12-11T11:46:32Z date_published: 2013-01-07T00:00:00Z date_updated: 2021-01-12T07:57:25Z day: '07' department: - _id: NiBa doi: 10.1098/rspb.2012.2058 external_id: pmid: - '23173202' intvolume: ' 280' issue: '1750' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/ month: '01' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '7372' quality_controlled: '1' status: public title: Source population characteristics affect heterosis following genetic rescue of fragmented plant populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 280 year: '2013' ... --- _id: '476' abstract: - lang: eng text: 'Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. ' author: - first_name: Desiree full_name: Dickerson, Desiree id: 444EB89E-F248-11E8-B48F-1D18A9856A87 last_name: Dickerson - first_name: David full_name: Bilkey, David last_name: Bilkey citation: ama: 'Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217' apa: 'Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217' chicago: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.' ieee: 'D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research Foundation, 2013.' ista: 'Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 7(DEC).' mla: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research Foundation, 2013, doi:10.3389/fnbeh.2013.00217.' short: D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013). date_created: 2018-12-11T11:46:41Z date_published: 2013-12-27T00:00:00Z date_updated: 2021-01-12T08:00:53Z day: '27' ddc: - '571' department: - _id: JoCs doi: 10.3389/fnbeh.2013.00217 file: - access_level: open_access checksum: cd7183121e56251176100ccac165c95c content_type: application/pdf creator: system date_created: 2018-12-12T10:15:10Z date_updated: 2020-07-14T12:46:35Z file_id: '5128' file_name: IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf file_size: 530134 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 7' issue: DEC language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Frontiers in Behavioral Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '7346' pubrep_id: '953' quality_controlled: '1' status: public title: 'Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2013' ... --- _id: '499' abstract: - lang: eng text: Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing "persisters." Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure. author: - first_name: Yurichi full_name: Wakamoto, Yurichi last_name: Wakamoto - first_name: Neraaj full_name: Dhar, Neraaj last_name: Dhar - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Katrin full_name: Schneider, Katrin last_name: Schneider - first_name: François full_name: Signorino Gelo, François last_name: Signorino Gelo - first_name: Stanislas full_name: Leibler, Stanislas last_name: Leibler - first_name: John full_name: Mckinney, John last_name: Mckinney citation: ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858 apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858 chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1229858. ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,” Science, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013. ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95. mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” Science, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:10.1126/science.1229858. short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95. date_created: 2018-12-11T11:46:48Z date_published: 2013-01-04T00:00:00Z date_updated: 2021-01-12T08:01:06Z day: '04' department: - _id: CaGu - _id: GaTk doi: 10.1126/science.1229858 intvolume: ' 339' issue: '6115' language: - iso: eng month: '01' oa_version: None page: 91 - 95 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '7321' quality_controlled: '1' scopus_import: 1 status: public title: Dynamic persistence of antibiotic-stressed mycobacteria type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2013' ... --- _id: '500' abstract: - lang: eng text: 'Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.' acknowledgement: "This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n" article_number: '222' author: - first_name: Melissa full_name: Ward, Melissa last_name: Ward - first_name: Samantha full_name: Lycett, Samantha last_name: Lycett - first_name: Dorita full_name: Avila, Dorita last_name: Avila - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Andrew full_name: Leigh Brown, Andrew last_name: Leigh Brown citation: ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-222 apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222 chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222. ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013. ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222. mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no. 1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222. short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013). date_created: 2018-12-11T11:46:49Z date_published: 2013-10-09T00:00:00Z date_updated: 2021-01-12T08:01:08Z day: '09' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-222 file: - access_level: open_access checksum: 52cf48a7c1794676ae8b0029573a84a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4722' file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf file_size: 1150052 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '7320' pubrep_id: '941' quality_controlled: '1' scopus_import: 1 status: public title: Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '501' abstract: - lang: eng text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.' author: - first_name: Mario full_name: Cozzuol, Mario last_name: Cozzuol - first_name: Camila full_name: Clozato, Camila last_name: Clozato - first_name: Elizete full_name: Holanda, Elizete last_name: Holanda - first_name: Flávio full_name: Rodrigues, Flávio last_name: Rodrigues - first_name: Samuel full_name: Nienow, Samuel last_name: Nienow - first_name: Benoit full_name: De Thoisy, Benoit last_name: De Thoisy - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Fabrício full_name: Santos, Fabrício last_name: Santos citation: ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1 apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1 chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1. ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013. ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345. mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:10.1644/12-MAMM-A-169.1. short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345. date_created: 2018-12-11T11:46:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T08:01:09Z day: '01' ddc: - '570' department: - _id: JoBo doi: 10.1644/12-MAMM-A-169.1 file: - access_level: open_access checksum: 8007815078dccac21ecd1cf73a269dc6 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:59Z date_updated: 2020-07-14T12:46:36Z file_id: '4980' file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf file_size: 1040765 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 94' issue: '6' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1331 - 1345 publication: Journal of Mammalogy publication_status: published publisher: Oxford University Press publist_id: '7319' pubrep_id: '940' quality_controlled: '1' scopus_import: 1 status: public title: A new species of tapir from the Amazon 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: 94 year: '2013' ... --- _id: '505' abstract: - lang: eng text: Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts. acknowledgement: "This study was performed within the Austrian Centre of Indus-\r\ntrial Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology Agency of the \ City of Vienna through the\r\nCOMET-Funding Program managed by the Austrian Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with the CLSM measurements." author: - first_name: Katrin full_name: Greimel, Katrin last_name: Greimel - first_name: Veronika full_name: Perz, Veronika last_name: Perz - first_name: Klaus full_name: Koren, Klaus id: 382FBD6A-F248-11E8-B48F-1D18A9856A87 last_name: Koren - first_name: Roland full_name: Feola, Roland last_name: Feola - first_name: Armin full_name: Temel, Armin last_name: Temel - first_name: Christian full_name: Sohar, Christian last_name: Sohar - first_name: Enrique full_name: Herrero Acero, Enrique last_name: Herrero Acero - first_name: Ingo full_name: Klimant, Ingo last_name: Klimant - first_name: Georg full_name: Guebitz, Georg last_name: Guebitz citation: ama: 'Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 2013;15(2):381-388. doi:10.1039/c2gc36666e' apa: 'Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz, G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36666e' chicago: 'Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel, Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36666e.' ieee: 'K. Greimel et al., “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.' ista: 'Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.' mla: 'Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 381–88, doi:10.1039/c2gc36666e.' short: K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero, I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388. date_created: 2018-12-11T11:46:51Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T08:01:11Z day: '01' department: - _id: HaJa doi: 10.1039/c2gc36666e intvolume: ' 15' issue: '2' language: - iso: eng month: '02' oa_version: None page: 381 - 388 publication: Green Chemistry publication_status: published publisher: Royal Society of Chemistry publist_id: '7313' quality_controlled: '1' scopus_import: 1 status: public title: 'Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '502' abstract: - lang: eng text: 'Blind signatures allow users to obtain signatures on messages hidden from the signer; moreover, the signer cannot link the resulting message/signature pair to the signing session. This paper presents blind signature schemes, in which the number of interactions between the user and the signer is minimal and whose blind signatures are short. Our schemes are defined over bilinear groups and are proved secure in the common-reference-string model without random oracles and under standard assumptions: CDH and the decision-linear assumption. (We also give variants over asymmetric groups based on similar assumptions.) The blind signatures are Waters signatures, which consist of 2 group elements. Moreover, we instantiate partially blind signatures, where the message consists of a part hidden from the signer and a commonly known public part, and schemes achieving perfect blindness. We propose new variants of blind signatures, such as signer-friendly partially blind signatures, where the public part can be chosen by the signer without prior agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated messages provided by independent sources. We also extend Waters signatures to non-binary alphabets by proving a new result on the underlying hash function. ' author: - first_name: Olivier full_name: Blazy, Olivier last_name: Blazy - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: David full_name: Pointcheval, David last_name: Pointcheval - first_name: Damien full_name: Vergnaud, Damien last_name: Vergnaud citation: ama: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. Journal of Computer Security. 2013;21(5):627-661. doi:10.3233/JCS-130477 apa: Blazy, O., Fuchsbauer, G., Pointcheval, D., & Vergnaud, D. (2013). Short blind signatures. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-130477 chicago: Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud. “Short Blind Signatures.” Journal of Computer Security. IOS Press, 2013. https://doi.org/10.3233/JCS-130477. ieee: O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,” Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013. ista: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures. Journal of Computer Security. 21(5), 627–661. mla: Blazy, Olivier, et al. “Short Blind Signatures.” Journal of Computer Security, vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:10.3233/JCS-130477. short: O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer Security 21 (2013) 627–661. date_created: 2018-12-11T11:46:50Z date_published: 2013-11-22T00:00:00Z date_updated: 2021-01-12T08:01:09Z day: '22' department: - _id: KrPi doi: 10.3233/JCS-130477 intvolume: ' 21' issue: '5' language: - iso: eng month: '11' oa_version: None page: 627 - 661 publication: Journal of Computer Security publication_status: published publisher: IOS Press publist_id: '7318' quality_controlled: '1' scopus_import: 1 status: public title: Short blind signatures type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2013' ... --- _id: '508' abstract: - lang: eng text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases. author: - first_name: Eduardo full_name: Tarazona Santos, Eduardo last_name: Tarazona Santos - first_name: Moara full_name: Machado, Moara last_name: Machado - first_name: Wagner full_name: Magalhães, Wagner last_name: Magalhães - first_name: Renee full_name: Chen, Renee last_name: Chen - first_name: Fernanda full_name: Lyon, Fernanda last_name: Lyon - first_name: Laurie full_name: Burdett, Laurie last_name: Burdett - first_name: Andrew full_name: Crenshaw, Andrew last_name: Crenshaw - first_name: Cristina full_name: Fabbri, Cristina last_name: Fabbri - first_name: Latife full_name: Pereira, Latife last_name: Pereira - first_name: Laelia full_name: Pinto, Laelia last_name: Pinto - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Ben full_name: Sestanovich, Ben last_name: Sestanovich - first_name: Meredith full_name: Yeager, Meredith last_name: Yeager - first_name: Stephen full_name: Chanock, Stephen last_name: Chanock citation: ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119' apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119' chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.' ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.' ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.' mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:10.1093/molbev/mst119.' short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167. date_created: 2018-12-11T11:46:52Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:01:12Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst119 external_id: pmid: - '23821607' intvolume: ' 30' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/ month: '09' oa: 1 oa_version: Submitted Version page: 2157 - 2167 pmid: 1 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '7310' quality_controlled: '1' scopus_import: 1 status: public title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2013' ... --- _id: '509' abstract: - lang: eng text: 'Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. ' author: - first_name: Simone full_name: Di Rubbo, Simone last_name: Di Rubbo - first_name: Niloufer full_name: Irani, Niloufer last_name: Irani - first_name: Soo full_name: Kim, Soo last_name: Kim - first_name: Zheng full_name: Xu, Zheng last_name: Xu - first_name: Astrid full_name: Gadeyne, Astrid last_name: Gadeyne - first_name: Wim full_name: Dejonghe, Wim last_name: Dejonghe - first_name: Isabelle full_name: Vanhoutte, Isabelle last_name: Vanhoutte - first_name: Geert full_name: Persiau, Geert last_name: Persiau - first_name: Dominique full_name: Eeckhout, Dominique last_name: Eeckhout - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Kyungyoung full_name: Song, Kyungyoung last_name: Song - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Daniël full_name: Van Damme, Daniël last_name: Van Damme - first_name: Inhwan full_name: Hwang, Inhwan last_name: Hwang - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 2013;25(8):2986-2997. doi:10.1105/tpc.113.114058 apa: Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova, E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114058 chicago: Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114058. ieee: S. Di Rubbo et al., “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013. ista: Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997. mla: Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:10.1105/tpc.113.114058. short: S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte, G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger, D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997. date_created: 2018-12-11T11:46:52Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:01:13Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.113.114058 external_id: pmid: - '23975899' intvolume: ' 25' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/ month: '08' oa: 1 oa_version: Submitted Version page: 2986 - 2997 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '7311' quality_controlled: '1' scopus_import: 1 status: public title: The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '507' abstract: - lang: eng text: Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs. author: - first_name: Soo full_name: Kim, Soo last_name: Kim - first_name: Zheng full_name: Xu, Zheng last_name: Xu - first_name: Kyungyoung full_name: Song, Kyungyoung last_name: Song - first_name: Dae full_name: Kim, Dae last_name: Kim - first_name: Hyangju full_name: Kang, Hyangju last_name: Kang - first_name: Ilka full_name: Reichardt, Ilka last_name: Reichardt - first_name: Eun full_name: Sohn, Eun last_name: Sohn - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Gerd full_name: Juergens, Gerd last_name: Juergens - first_name: Inhwan full_name: Hwang, Inhwan last_name: Hwang citation: ama: Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 2013;25(8):2970-2985. doi:10.1105/tpc.113.114264 apa: Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114264 chicago: Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114264. ieee: S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” Plant Cell, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013. ista: Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985. mla: Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” Plant Cell, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:10.1105/tpc.113.114264. short: S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985. date_created: 2018-12-11T11:46:52Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:01:12Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.113.114264 external_id: pmid: - '23975898' intvolume: ' 25' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/ month: '08' oa: 1 oa_version: Submitted Version page: 2970 - 2985 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '7312' quality_controlled: '1' scopus_import: 1 status: public title: Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '511' abstract: - lang: eng text: The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms. author: - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Biljana full_name: Simonovik, Biljana last_name: Simonovik - first_name: Sara full_name: Petersson, Sara last_name: Petersson - first_name: Eva full_name: Henyková, Eva last_name: Henyková - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Kathleen full_name: Greenham, Kathleen last_name: Greenham - first_name: Yi full_name: Zhang, Yi last_name: Zhang - first_name: Mariusz full_name: Kowalczyk, Mariusz last_name: Kowalczyk - first_name: Mark full_name: Estelle, Mark last_name: Estelle - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Göran full_name: Sandberg, Göran last_name: Sandberg - first_name: Karin full_name: Ljung, Karin last_name: Ljung citation: ama: Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 2013;25(10):3858-3870. doi:10.1105/tpc.113.114421 apa: Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham, K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114421 chicago: Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon, Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114421. ieee: A. Pěnčík et al., “Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid,” Plant Cell, vol. 25, no. 10. American Society of Plant Biologists, pp. 3858–3870, 2013. ista: Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10), 3858–3870. mla: Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” Plant Cell, vol. 25, no. 10, American Society of Plant Biologists, 2013, pp. 3858–70, doi:10.1105/tpc.113.114421. short: A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham, Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung, Plant Cell 25 (2013) 3858–3870. date_created: 2018-12-11T11:46:53Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T08:01:15Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.113.114421 external_id: pmid: - '24163311' intvolume: ' 25' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: www.doi.org/10.1105/tpc.113.114421 month: '10' oa: 1 oa_version: Published Version page: 3858 - 3870 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '7309' quality_controlled: '1' scopus_import: 1 status: public title: Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '516' abstract: - lang: eng text: In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development. article_number: '688' article_processing_charge: No author: - first_name: Bastiaan full_name: Bargmann, Bastiaan last_name: Bargmann - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Gabriel full_name: Krouk, Gabriel last_name: Krouk - first_name: Tal full_name: Nawy, Tal last_name: Nawy - first_name: Idan full_name: Efroni, Idan last_name: Efroni - first_name: Eilon full_name: Shani, Eilon last_name: Shani - first_name: Goh full_name: Choe, Goh last_name: Choe - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dominique full_name: Bergmann, Dominique last_name: Bergmann - first_name: Mark full_name: Estelle, Mark last_name: Estelle - first_name: Kenneth full_name: Birnbaum, Kenneth last_name: Birnbaum citation: ama: Bargmann B, Vanneste S, Krouk G, et al. A map of cell type‐specific auxin responses. Molecular Systems Biology. 2013;9(1). doi:10.1038/msb.2013.40 apa: Bargmann, B., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., … Birnbaum, K. (2013). A map of cell type‐specific auxin responses. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2013.40 chicago: Bargmann, Bastiaan, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.40. ieee: B. Bargmann et al., “A map of cell type‐specific auxin responses,” Molecular Systems Biology, vol. 9, no. 1. Nature Publishing Group, 2013. ista: Bargmann B, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann D, Estelle M, Birnbaum K. 2013. A map of cell type‐specific auxin responses. Molecular Systems Biology. 9(1), 688. mla: Bargmann, Bastiaan, et al. “A Map of Cell Type‐specific Auxin Responses.” Molecular Systems Biology, vol. 9, no. 1, 688, Nature Publishing Group, 2013, doi:10.1038/msb.2013.40. short: B. Bargmann, S. Vanneste, G. Krouk, T. Nawy, I. Efroni, E. Shani, G. Choe, J. Friml, D. Bergmann, M. Estelle, K. Birnbaum, Molecular Systems Biology 9 (2013). date_created: 2018-12-11T11:46:55Z date_published: 2013-09-10T00:00:00Z date_updated: 2021-01-12T08:01:17Z day: '10' ddc: - '581' department: - _id: JiFr doi: 10.1038/msb.2013.40 file: - access_level: open_access checksum: 9c4fbe793af4bb22b3fe50cc677a39bf content_type: application/pdf creator: system date_created: 2018-12-12T10:07:46Z date_updated: 2020-07-14T12:46:36Z file_id: '4644' file_name: IST-2018-936-v1+1_2008_Barton_A_map.pdf file_size: 3257692 relation: main_file file_date_updated: 2020-07-14T12:46:36Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '09' oa: 1 oa_version: Published Version publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '7303' pubrep_id: '936' quality_controlled: '1' scopus_import: 1 status: public title: A map of cell type‐specific auxin responses tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '522' abstract: - lang: eng text: Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic endothelial cells and responsible for separation of blood and lymphatic circulation through activation of platelets. Here we show that podoplanin is also expressed by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell type associated with thymic conduits, and involved in development of natural regulatory T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes in the medulla. This might be due to CCL21 that delocalizes upon deletion of the CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not remain devoid of nTreg but generate them delayed within the first month resulting in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype of Foxp3-deficient Scurfy mice. author: - first_name: Elke full_name: Fuertbauer, Elke last_name: Fuertbauer - first_name: Jan full_name: Zaujec, Jan last_name: Zaujec - first_name: Pavel full_name: Uhrin, Pavel last_name: Uhrin - first_name: Ingrid full_name: Raab, Ingrid last_name: Raab - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Helga full_name: Schachner, Helga last_name: Schachner - first_name: Miroslav full_name: Bauer, Miroslav last_name: Bauer - first_name: Gerhard full_name: Schütz, Gerhard last_name: Schütz - first_name: Bernd full_name: Binder, Bernd last_name: Binder - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Dontscho full_name: Kerjaschki, Dontscho last_name: Kerjaschki - first_name: Hannes full_name: Stockinger, Hannes last_name: Stockinger citation: ama: Fuertbauer E, Zaujec J, Uhrin P, et al. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 2013;154(1-2):31-41. doi:10.1016/j.imlet.2013.07.007 apa: Fuertbauer, E., Zaujec, J., Uhrin, P., Raab, I., Weber, M., Schachner, H., … Stockinger, H. (2013). Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. Elsevier. https://doi.org/10.1016/j.imlet.2013.07.007 chicago: Fuertbauer, Elke, Jan Zaujec, Pavel Uhrin, Ingrid Raab, Michele Weber, Helga Schachner, Miroslav Bauer, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” Immunology Letters. Elsevier, 2013. https://doi.org/10.1016/j.imlet.2013.07.007. ieee: E. Fuertbauer et al., “Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells,” Immunology Letters, vol. 154, no. 1–2. Elsevier, pp. 31–41, 2013. ista: Fuertbauer E, Zaujec J, Uhrin P, Raab I, Weber M, Schachner H, Bauer M, Schütz G, Binder B, Sixt MK, Kerjaschki D, Stockinger H. 2013. Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells. Immunology Letters. 154(1–2), 31–41. mla: Fuertbauer, Elke, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes Natural Regulatory T Cells.” Immunology Letters, vol. 154, no. 1–2, Elsevier, 2013, pp. 31–41, doi:10.1016/j.imlet.2013.07.007. short: E. Fuertbauer, J. Zaujec, P. Uhrin, I. Raab, M. Weber, H. Schachner, M. Bauer, G. Schütz, B. Binder, M.K. Sixt, D. Kerjaschki, H. Stockinger, Immunology Letters 154 (2013) 31–41. date_created: 2018-12-11T11:46:57Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:01:22Z day: '01' department: - _id: MiSi doi: 10.1016/j.imlet.2013.07.007 intvolume: ' 154' issue: 1-2 language: - iso: eng month: '07' oa_version: None page: 31 - 41 publication: Immunology Letters publication_status: published publisher: Elsevier publist_id: '7300' quality_controlled: '1' scopus_import: 1 status: public title: Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 154 year: '2013' ... --- _id: '2279' abstract: - lang: eng text: We consider two-player games played on weighted directed graphs with mean-payoff and total-payoff objectives, two classical quantitative objectives. While for single-dimensional games the complexity and memory bounds for both objectives coincide, we show that in contrast to multi-dimensional mean-payoff games that are known to be coNP-complete, multi-dimensional total-payoff games are undecidable. We introduce conservative approximations of these objectives, where the payoff is considered over a local finite window sliding along a play, instead of the whole play. For single dimension, we show that (i) if the window size is polynomial, deciding the winner takes polynomial time, and (ii) the existence of a bounded window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff games. For multiple dimensions, we show that (i) the problem with fixed window size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to decide the existence of a bounded window. acknowledgement: 279307; ERC; Fonds National de la Reserche Luxembourg; 279499; ERC; Fonds National de la Reserche Luxembourg 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: Mickael full_name: Randour, Mickael last_name: Randour - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff through windows. 2013;8172:118-132. doi:10.1007/978-3-319-02444-8_10 apa: 'Chatterjee, K., Doyen, L., Randour, M., & Raskin, J. (2013). Looking at mean-payoff and total-payoff through windows. Presented at the ATVA: Automated Technology for Verification and Analysis, Hanoi, Vietnam: Springer. https://doi.org/10.1007/978-3-319-02444-8_10' chicago: Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin. “Looking at Mean-Payoff and Total-Payoff through Windows.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-319-02444-8_10. ieee: K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff and total-payoff through windows,” vol. 8172. Springer, pp. 118–132, 2013. ista: Chatterjee K, Doyen L, Randour M, Raskin J. 2013. Looking at mean-payoff and total-payoff through windows. 8172, 118–132. mla: Chatterjee, Krishnendu, et al. Looking at Mean-Payoff and Total-Payoff through Windows. Vol. 8172, Springer, 2013, pp. 118–32, doi:10.1007/978-3-319-02444-8_10. short: K. Chatterjee, L. Doyen, M. Randour, J. Raskin, 8172 (2013) 118–132. conference: end_date: 2013-10-18 location: Hanoi, Vietnam name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2013-10-15 date_created: 2018-12-11T11:56:44Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-23T12:22:51Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-319-02444-8_10 ec_funded: 1 intvolume: ' 8172' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1302.4248 month: '01' oa: 1 oa_version: Preprint page: 118 - 132 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '4656' quality_controlled: '1' related_material: record: - id: '523' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Looking at mean-payoff and total-payoff through windows type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8172 year: '2013' ... --- _id: '528' abstract: - lang: eng text: Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin [1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal axis [3-6]. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis [9-12]. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life [13, 14]. author: - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Anna full_name: Stepanova, Anna last_name: Stepanova - first_name: Linda full_name: Robles, Linda last_name: Robles - first_name: Annemarie full_name: Lokerse, Annemarie last_name: Lokerse - first_name: Jose full_name: Alonso, Jose last_name: Alonso - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Robert H, Grones P, Stepanova A, et al. Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. 2013;23(24):2506-2512. doi:10.1016/j.cub.2013.09.039 apa: Robert, H., Grones, P., Stepanova, A., Robles, L., Lokerse, A., Alonso, J., … Friml, J. (2013). Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.09.039 chicago: Robert, Hélène, Peter Grones, Anna Stepanova, Linda Robles, Annemarie Lokerse, Jose Alonso, Dolf Weijers, and Jiří Friml. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.09.039. ieee: H. Robert et al., “Local auxin sources orient the apical basal axis in arabidopsis embryos,” Current Biology, vol. 23, no. 24. Cell Press, pp. 2506–2512, 2013. ista: Robert H, Grones P, Stepanova A, Robles L, Lokerse A, Alonso J, Weijers D, Friml J. 2013. Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. 23(24), 2506–2512. mla: Robert, Hélène, et al. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” Current Biology, vol. 23, no. 24, Cell Press, 2013, pp. 2506–12, doi:10.1016/j.cub.2013.09.039. short: H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D. Weijers, J. Friml, Current Biology 23 (2013) 2506–2512. date_created: 2018-12-11T11:46:59Z date_published: 2013-12-16T00:00:00Z date_updated: 2021-01-12T08:01:25Z day: '16' department: - _id: JiFr doi: 10.1016/j.cub.2013.09.039 ec_funded: 1 intvolume: ' 23' issue: '24' language: - iso: eng month: '12' oa_version: None page: 2506 - 2512 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Current Biology publication_status: published publisher: Cell Press publist_id: '7291' quality_controlled: '1' scopus_import: 1 status: public title: Local auxin sources orient the apical basal axis in arabidopsis embryos type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '527' abstract: - lang: eng text: The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development. author: - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Richard full_name: Smith, Richard last_name: Smith - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 2013;23(24):2513-2518. doi:10.1016/j.cub.2013.10.038 apa: Wabnik, K. T., Robert, H., Smith, R., & Friml, J. (2013). Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.10.038 chicago: Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.10.038. ieee: K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the establishment of the apical-basal embryonic axis in plants,” Current Biology, vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013. ista: Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518. mla: Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” Current Biology, vol. 23, no. 24, Cell Press, 2013, pp. 2513–18, doi:10.1016/j.cub.2013.10.038. short: K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518. date_created: 2018-12-11T11:46:58Z date_published: 2013-12-16T00:00:00Z date_updated: 2021-01-12T08:01:24Z day: '16' department: - _id: EvBe - _id: JiFr doi: 10.1016/j.cub.2013.10.038 ec_funded: 1 intvolume: ' 23' issue: '24' language: - iso: eng month: '12' oa_version: None page: 2513 - 2518 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Current Biology publication_status: published publisher: Cell Press publist_id: '7292' quality_controlled: '1' scopus_import: 1 status: public title: Modeling framework for the establishment of the apical-basal embryonic axis in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '5399' abstract: - lang: eng text: In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics. alternative_title: - IST Austria Technical Report author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Ivana full_name: Bozic, Ivana last_name: Bozic - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: 'Reiter J, Bozic I, Chatterjee K, Nowak M. TTP: Tool for Tumor Progression. IST Austria; 2013. doi:10.15479/AT:IST-2013-104-v1-1' apa: 'Reiter, J., Bozic, I., Chatterjee, K., & Nowak, M. (2013). TTP: Tool for Tumor Progression. IST Austria. https://doi.org/10.15479/AT:IST-2013-104-v1-1' chicago: 'Reiter, Johannes, Ivana Bozic, Krishnendu Chatterjee, and Martin Nowak. TTP: Tool for Tumor Progression. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-104-v1-1.' ieee: 'J. Reiter, I. Bozic, K. Chatterjee, and M. Nowak, TTP: Tool for Tumor Progression. IST Austria, 2013.' ista: 'Reiter J, Bozic I, Chatterjee K, Nowak M. 2013. TTP: Tool for Tumor Progression, IST Austria, 17p.' mla: 'Reiter, Johannes, et al. TTP: Tool for Tumor Progression. IST Austria, 2013, doi:10.15479/AT:IST-2013-104-v1-1.' short: 'J. Reiter, I. Bozic, K. Chatterjee, M. Nowak, TTP: Tool for Tumor Progression, IST Austria, 2013.' date_created: 2018-12-12T11:39:07Z date_published: 2013-01-11T00:00:00Z date_updated: 2023-02-23T10:23:57Z day: '11' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2013-104-v1-1 file: - access_level: open_access checksum: 2cc8c6e157eca1271128db80bb3dec80 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:20Z date_updated: 2020-07-14T12:46:44Z file_id: '5542' file_name: IST-2013-104-v1+1_tumortool.pdf file_size: 1471954 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '17' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '104' related_material: record: - id: '2000' relation: later_version status: public status: public title: 'TTP: Tool for Tumor Progression' type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2295' abstract: - lang: eng text: We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal EXPTIME-complete complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite-memory strategies. We also establish asymptotically optimal (exponential) memory bounds. alternative_title: - LIPIcs 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: Mathieu full_name: Tracol, Mathieu id: 3F54FA38-F248-11E8-B48F-1D18A9856A87 last_name: Tracol citation: ama: Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with omega-regular objectives. 2013;23:165-180. doi:10.4230/LIPIcs.CSL.2013.165 apa: 'Chatterjee, K., Chmelik, M., & Tracol, M. (2013). What is decidable about partially observable Markov decision processes with omega-regular objectives. Presented at the CSL: Computer Science Logic, Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2013.165' chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with Omega-Regular Objectives.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.165. ieee: K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with omega-regular objectives,” vol. 23. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 165–180, 2013. ista: Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with omega-regular objectives. 23, 165–180. mla: Chatterjee, Krishnendu, et al. What Is Decidable about Partially Observable Markov Decision Processes with Omega-Regular Objectives. Vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 165–80, doi:10.4230/LIPIcs.CSL.2013.165. short: K. Chatterjee, M. Chmelik, M. Tracol, 23 (2013) 165–180. conference: end_date: 2013-09-05 location: Torino, Italy name: 'CSL: Computer Science Logic' start_date: 2013-09-02 date_created: 2018-12-11T11:56:50Z date_published: 2013-08-27T00:00:00Z date_updated: 2023-02-23T12:24:38Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPIcs.CSL.2013.165 ec_funded: 1 file: - access_level: open_access checksum: ba2828322955574d9283bea0e17a37a6 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:42Z date_updated: 2020-07-14T12:45:37Z file_id: '4766' file_name: IST-2017-756-v1+1_2.pdf file_size: 345171 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 23' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 165 - 180 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: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4633' pubrep_id: '756' quality_controlled: '1' related_material: record: - id: '1477' relation: later_version status: public - id: '5400' relation: earlier_version status: public scopus_import: 1 series_title: Leibniz International Proceedings in Informatics status: public title: What is decidable about partially observable Markov decision processes with omega-regular objectives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '5403' abstract: - lang: eng text: 'We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of mean-payoff games) that is not known to be in polynomial 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 citation: ama: Chatterjee K, Ibsen-Jensen R. Qualitative Analysis of Concurrent Mean-Payoff Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-126-v1-1 apa: Chatterjee, K., & Ibsen-Jensen, R. (2013). Qualitative analysis of concurrent mean-payoff games. IST Austria. https://doi.org/10.15479/AT:IST-2013-126-v1-1 chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. Qualitative Analysis of Concurrent Mean-Payoff Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-126-v1-1. ieee: K. Chatterjee and R. Ibsen-Jensen, Qualitative analysis of concurrent mean-payoff games. IST Austria, 2013. ista: Chatterjee K, Ibsen-Jensen R. 2013. Qualitative analysis of concurrent mean-payoff games, IST Austria, 33p. mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. Qualitative Analysis of Concurrent Mean-Payoff Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-126-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, Qualitative Analysis of Concurrent Mean-Payoff Games, IST Austria, 2013. date_created: 2018-12-12T11:39:08Z date_published: 2013-07-03T00:00:00Z date_updated: 2023-02-23T12:22:53Z day: '03' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-126-v1-1 file: - access_level: open_access checksum: 063868c665beec37bf28160e2a695746 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:49Z date_updated: 2020-07-14T12:46:45Z file_id: '5510' file_name: IST-2013-126-v1+1_soda_full.pdf file_size: 434523 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '33' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '126' related_material: record: - id: '524' relation: later_version status: public status: public title: Qualitative analysis of concurrent mean-payoff games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5402' abstract: - lang: eng text: "Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element. \r\nIn this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention." 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: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: Henzinger TA, Sezgin A. How Free Is Your Linearizable Concurrent Data Structure? IST Austria; 2013. doi:10.15479/AT:IST-2013-123-v1-1 apa: Henzinger, T. A., & Sezgin, A. (2013). How free is your linearizable concurrent data structure? IST Austria. https://doi.org/10.15479/AT:IST-2013-123-v1-1 chicago: Henzinger, Thomas A, and Ali Sezgin. How Free Is Your Linearizable Concurrent Data Structure? IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-123-v1-1. ieee: T. A. Henzinger and A. Sezgin, How free is your linearizable concurrent data structure? IST Austria, 2013. ista: Henzinger TA, Sezgin A. 2013. How free is your linearizable concurrent data structure?, IST Austria, 16p. mla: Henzinger, Thomas A., and Ali Sezgin. How Free Is Your Linearizable Concurrent Data Structure? IST Austria, 2013, doi:10.15479/AT:IST-2013-123-v1-1. short: T.A. Henzinger, A. Sezgin, How Free Is Your Linearizable Concurrent Data Structure?, IST Austria, 2013. date_created: 2018-12-12T11:39:07Z date_published: 2013-06-12T00:00:00Z date_updated: 2020-07-14T23:04:47Z day: '12' ddc: - '000' - '004' department: - _id: ToHe doi: 10.15479/AT:IST-2013-123-v1-1 file: - access_level: open_access checksum: ce580605ae9756a8c99d7b403ebb8eed content_type: application/pdf creator: system date_created: 2018-12-12T11:53:19Z date_updated: 2020-07-14T12:46:45Z file_id: '5480' file_name: IST-2013-123-v1+1_main-concur2013.pdf file_size: 249790 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '16' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '123' status: public title: How free is your linearizable concurrent data structure? type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5400' abstract: - lang: eng text: We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. 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: Mathieu full_name: Tracol, Mathieu id: 3F54FA38-F248-11E8-B48F-1D18A9856A87 last_name: Tracol citation: ama: Chatterjee K, Chmelik M, Tracol M. What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives. IST Austria; 2013. doi:10.15479/AT:IST-2013-109-v1-1 apa: Chatterjee, K., Chmelik, M., & Tracol, M. (2013). What is decidable about partially observable Markov decision processes with ω-regular objectives. IST Austria. https://doi.org/10.15479/AT:IST-2013-109-v1-1 chicago: Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-109-v1-1. ieee: K. Chatterjee, M. Chmelik, and M. Tracol, What is decidable about partially observable Markov decision processes with ω-regular objectives. IST Austria, 2013. ista: Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with ω-regular objectives, IST Austria, 41p. mla: Chatterjee, Krishnendu, et al. What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives. IST Austria, 2013, doi:10.15479/AT:IST-2013-109-v1-1. short: K. Chatterjee, M. Chmelik, M. Tracol, What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives, IST Austria, 2013. date_created: 2018-12-12T11:39:07Z date_published: 2013-02-20T00:00:00Z date_updated: 2023-02-23T10:36:45Z day: '20' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-109-v1-1 file: - access_level: open_access checksum: cbba40210788a1b22c6cf06433b5ed6f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:06Z date_updated: 2020-07-14T12:46:44Z file_id: '5467' file_name: IST-2013-109-v1+1_What_is_Decidable_about_Partially_Observable_Markov_Decision_Processes_with_ω-Regular_Objectives.pdf file_size: 483407 relation: main_file file_date_updated: 2020-07-14T12:46:44Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '41' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '109' related_material: record: - id: '1477' relation: later_version status: public - id: '2295' relation: later_version status: public status: public title: What is decidable about partially observable Markov decision processes with ω-regular objectives type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5404' abstract: - lang: eng text: 'We study finite-state two-player (zero-sum) concurrent mean-payoff games played on a 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 lie in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP and coNP is the long-standing best known bound). We show that the exact value can be expressed in the existential theory of the reals, and also establish square-root sum hardness for a related class of games.' 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 Complexity of Ergodic Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-127-v1-1 apa: Chatterjee, K., & Ibsen-Jensen, R. (2013). The complexity of ergodic games. IST Austria. https://doi.org/10.15479/AT:IST-2013-127-v1-1 chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-127-v1-1. ieee: K. Chatterjee and R. Ibsen-Jensen, The complexity of ergodic games. IST Austria, 2013. ista: Chatterjee K, Ibsen-Jensen R. 2013. The complexity of ergodic games, IST Austria, 29p. mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Ergodic Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-127-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, The Complexity of Ergodic Games, IST Austria, 2013. date_created: 2018-12-12T11:39:08Z date_published: 2013-07-03T00:00:00Z date_updated: 2023-02-23T10:30:55Z day: '03' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-127-v1-1 file: - access_level: open_access checksum: 79ee5e677a82611ce06e0360c69d494a content_type: application/pdf creator: system date_created: 2018-12-12T11:53:35Z date_updated: 2020-07-14T12:46:45Z file_id: '5496' file_name: IST-2013-127-v1+1_ergodic.pdf file_size: 517275 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '29' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '127' related_material: record: - id: '2162' relation: later_version status: public status: public title: The complexity of ergodic games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5401' abstract: - lang: eng text: This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the actual initiatives, projects and standards related to the project. It supports the preparation of standards and specifications for the project, which should be considered and followed to ensure interoperability and visibility of the uploaded data. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Initiatives and Projects Related to RD. IST Austria; 2013. apa: Porsche, J. (2013). Initiatives and projects related to RD. IST Austria. chicago: Porsche, Jana. Initiatives and Projects Related to RD. IST Austria, 2013. ieee: J. Porsche, Initiatives and projects related to RD. IST Austria, 2013. ista: Porsche J. 2013. Initiatives and projects related to RD, IST Austria,p. mla: Porsche, Jana. Initiatives and Projects Related to RD. IST Austria, 2013. short: J. Porsche, Initiatives and Projects Related to RD, IST Austria, 2013. date_created: 2018-12-12T11:39:07Z date_published: 2013-03-20T00:00:00Z date_updated: 2020-07-14T23:04:47Z day: '20' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: d68712db838432ecdacf9ffb1de8f8a6 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:14Z date_updated: 2020-07-14T12:46:45Z file_id: '5536' file_name: IST-2013-113-v1+1_Initiatives_and_projects_related_to_RD.pdf file_size: 151208 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria pubrep_id: '113' status: public title: Initiatives and projects related to RD type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5405' 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) with only parity objectives, or with only mean-payoff objectives. We present an algorithm running\r\nin time O(d · n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the objective\r\ncan be ensured with probability 1, where n is the number of states of the game, d the number of priorities\r\nof the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states\r\nin 2-1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems\r\nwith both functional requirement (given as a qualitative objective) and performance requirement (given\r\nas a quantitative objective)." 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 - 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. IST Austria; 2013. doi:10.15479/AT:IST-2013-128-v1-1 apa: Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2013). Perfect-information stochastic mean-payoff parity games. IST Austria. https://doi.org/10.15479/AT:IST-2013-128-v1-1 chicago: Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. Perfect-Information Stochastic Mean-Payoff Parity Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-128-v1-1. ieee: K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, Perfect-information stochastic mean-payoff parity games. IST Austria, 2013. ista: Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2013. Perfect-information stochastic mean-payoff parity games, IST Austria, 22p. mla: Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff Parity Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-128-v1-1. short: K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, Perfect-Information Stochastic Mean-Payoff Parity Games, IST Austria, 2013. date_created: 2018-12-12T11:39:09Z date_published: 2013-07-08T00:00:00Z date_updated: 2023-02-23T10:33:08Z day: '08' ddc: - '000' - '005' - '510' department: - _id: KrCh doi: 10.15479/AT:IST-2013-128-v1-1 file: - access_level: open_access checksum: ede787a10e74e4f7db302fab8f12f3ca content_type: application/pdf creator: system date_created: 2018-12-12T11:53:54Z date_updated: 2020-07-14T12:46:45Z file_id: '5516' file_name: IST-2013-128-v1+1_full_stoch_mpp.pdf file_size: 387467 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '22' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '128' related_material: record: - id: '2212' relation: later_version status: public status: public title: Perfect-information stochastic mean-payoff parity games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5409' 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. \r\nIn 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 timestamps. 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 delta away from the parameter, for delta>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 we show analogous decidability results for rectangular automata." 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: Rupak full_name: Majumdar, Rupak last_name: Majumdar citation: ama: Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit Distance for Timed Automata. IST Austria; 2013. doi:10.15479/AT:IST-2013-144-v1-1 apa: Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2013). Edit distance for timed automata. IST Austria. https://doi.org/10.15479/AT:IST-2013-144-v1-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Rupak Majumdar. Edit Distance for Timed Automata. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-144-v1-1. ieee: K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, Edit distance for timed automata. IST Austria, 2013. ista: Chatterjee K, Ibsen-Jensen R, Majumdar R. 2013. Edit distance for timed automata, IST Austria, 12p. mla: Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. IST Austria, 2013, doi:10.15479/AT:IST-2013-144-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, Edit Distance for Timed Automata, IST Austria, 2013. date_created: 2018-12-12T11:39:10Z date_published: 2013-10-30T00:00:00Z date_updated: 2023-02-23T10:33:18Z day: '30' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2013-144-v1-1 file: - access_level: open_access checksum: 0f7633081ba8299c543322f0ad08571f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:08Z date_updated: 2020-07-14T12:46:46Z file_id: '5469' file_name: IST-2013-144-v1+1_main.pdf file_size: 336377 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '12' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '144' related_material: record: - id: '2216' relation: later_version status: public status: public title: Edit distance for timed automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '1376' abstract: - lang: eng text: 'We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.' 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 - 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, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: 13th International Conference on Formal Methods in Computer-Aided Design. IEEE; 2013:18-25. doi:10.1109/FMCAD.2013.6679386' apa: 'Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In 13th International Conference on Formal Methods in Computer-Aided Design (pp. 18–25). Portland, OR, United States: IEEE. https://doi.org/10.1109/FMCAD.2013.6679386' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In 13th International Conference on Formal Methods in Computer-Aided Design, 18–25. IEEE, 2013. https://doi.org/10.1109/FMCAD.2013.6679386. ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in 13th International Conference on Formal Methods in Computer-Aided Design, Portland, OR, United States, 2013, pp. 18–25. ista: 'Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.' mla: Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25, doi:10.1109/FMCAD.2013.6679386. short: K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25. conference: end_date: 2013-10-23 location: Portland, OR, United States name: 'FMCAD: Formal Methods in Computer-Aided Design' start_date: 2013-10-20 date_created: 2018-12-11T11:51:40Z date_published: 2013-12-11T00:00:00Z date_updated: 2023-02-23T12:24:53Z day: '11' department: - _id: KrCh - _id: ToHe doi: 10.1109/FMCAD.2013.6679386 ec_funded: 1 language: - iso: eng month: '12' oa_version: None page: 18 - 25 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _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: 13th International Conference on Formal Methods in Computer-Aided Design publication_status: published publisher: IEEE publist_id: '5835' quality_controlled: '1' related_material: record: - id: '5406' relation: earlier_version status: public status: public title: Distributed synthesis for LTL fragments type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5406' abstract: - lang: eng text: 'We consider the distributed synthesis problem fortemporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTLand our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3)Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.' 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 - 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, Henzinger TA, Otop J, Pavlogiannis A. Distributed Synthesis for LTL Fragments. IST Austria; 2013. doi:10.15479/AT:IST-2013-130-v1-1 apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Pavlogiannis, A. (2013). Distributed synthesis for LTL Fragments. IST Austria. https://doi.org/10.15479/AT:IST-2013-130-v1-1 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. Distributed Synthesis for LTL Fragments. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-130-v1-1. ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, Distributed synthesis for LTL Fragments. IST Austria, 2013. ista: Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL Fragments, IST Austria, 11p. mla: Chatterjee, Krishnendu, et al. Distributed Synthesis for LTL Fragments. IST Austria, 2013, doi:10.15479/AT:IST-2013-130-v1-1. short: K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, Distributed Synthesis for LTL Fragments, IST Austria, 2013. date_created: 2018-12-12T11:39:09Z date_published: 2013-07-08T00:00:00Z date_updated: 2023-02-21T17:01:26Z day: '08' ddc: - '005' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2013-130-v1-1 file: - access_level: open_access checksum: 855513ebaf6f72228800c5fdb522f93c content_type: application/pdf creator: system date_created: 2018-12-12T11:54:18Z date_updated: 2020-07-14T12:46:45Z file_id: '5540' file_name: IST-2013-130-v1+1_Distributed_Synthesis.pdf file_size: 467895 relation: main_file file_date_updated: 2020-07-14T12:46:45Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '11' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '130' related_material: record: - id: '1376' relation: later_version status: public status: public title: Distributed synthesis for LTL Fragments type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5408' abstract: - lang: eng text: "We consider two-player partial-observation stochastic games where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are omega-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). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, they were shown to be decidable in 2EXPTIME under finite-memory strategies. We improve the complexity and show that the qualitative analysis problems for partial-observation stochastic parity games under finite-memory strategies are \r\nEXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis. " 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 - 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. IST Austria; 2013. doi:10.15479/AT:IST-2013-141-v1-1 apa: Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2013). The complexity of partial-observation stochastic parity games with finite-memory strategies. IST Austria. https://doi.org/10.15479/AT:IST-2013-141-v1-1 chicago: Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-141-v1-1. ieee: K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, The complexity of partial-observation stochastic parity games with finite-memory strategies. IST Austria, 2013. ista: Chatterjee K, Doyen L, Nain S, Vardi M. 2013. The complexity of partial-observation stochastic parity games with finite-memory strategies, IST Austria, 17p. mla: Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. IST Austria, 2013, doi:10.15479/AT:IST-2013-141-v1-1. short: K. Chatterjee, L. Doyen, S. Nain, M. Vardi, The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies, IST Austria, 2013. date_created: 2018-12-12T11:39:10Z date_published: 2013-09-12T00:00:00Z date_updated: 2023-02-23T10:33:11Z day: '12' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-141-v1-1 file: - access_level: open_access checksum: 226bc791124f8d3138379778ce834e86 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:16Z date_updated: 2020-07-14T12:46:46Z file_id: '5477' file_name: IST-2013-141-v1+1_main-tech-rpt.pdf file_size: 300481 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '17' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '141' related_material: record: - id: '2213' relation: later_version status: public status: public title: The complexity of partial-observation stochastic parity games with finite-memory strategies type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5407' abstract: - lang: eng text: This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled to provide an institutional repository as a platform and also a service to the scientists at the institute. It also includes optional features, which would be of strong benefit for the scientists and would increase the usage of the repository, and hence the visibility of research at IST Austria. author: - first_name: Jana full_name: Porsche, Jana id: 3252EDC2-F248-11E8-B48F-1D18A9856A87 last_name: Porsche citation: ama: Porsche J. Technical Requirements and Features. IST Austria; 2013. apa: Porsche, J. (2013). Technical requirements and features. IST Austria. chicago: Porsche, Jana. Technical Requirements and Features. IST Austria, 2013. ieee: J. Porsche, Technical requirements and features. IST Austria, 2013. ista: Porsche J. 2013. Technical requirements and features, IST Austria,p. mla: Porsche, Jana. Technical Requirements and Features. IST Austria, 2013. short: J. Porsche, Technical Requirements and Features, IST Austria, 2013. date_created: 2018-12-12T11:39:09Z date_published: 2013-07-13T00:00:00Z date_updated: 2020-07-14T23:07:51Z day: '13' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: 9e4f9abf79a56f651f0012a34909880f content_type: application/pdf creator: system date_created: 2018-12-12T11:53:02Z date_updated: 2020-07-14T12:46:46Z file_id: '5463' file_name: IST-2013-135-v1+1_Features.pdf file_size: 90311 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria pubrep_id: '135' status: public title: Technical requirements and features type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '5410' abstract: - lang: eng text: "Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. \r\nOur approach generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. " alternative_title: - IST Austria Technical Report author: - first_name: Umair full_name: Ahmed, Umair last_name: Ahmed - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Sumit full_name: Gulwani, Sumit last_name: Gulwani citation: ama: Ahmed U, Chatterjee K, Gulwani S. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-146-v1-1 apa: Ahmed, U., Chatterjee, K., & Gulwani, S. (2013). Automatic generation of alternative starting positions for traditional board games. IST Austria. https://doi.org/10.15479/AT:IST-2013-146-v1-1 chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-146-v1-1. ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative starting positions for traditional board games. IST Austria, 2013. ista: Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p. mla: Ahmed, Umair, et al. Automatic Generation of Alternative Starting Positions for Traditional Board Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-146-v1-1. short: U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013. date_created: 2018-12-12T11:39:10Z date_published: 2013-12-03T00:00:00Z date_updated: 2023-02-23T10:00:50Z day: '03' ddc: - '000' - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2013-146-v1-1 file: - access_level: open_access checksum: 409f3aaaf1184e4057b89cbb449dac80 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:06Z date_updated: 2020-07-14T12:46:46Z file_id: '5528' file_name: IST-2013-146-v1+1_main.pdf file_size: 818189 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '13' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '146' related_material: record: - id: '1481' relation: later_version status: public status: public title: Automatic generation of alternative starting positions for traditional board games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2327' 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. The 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. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We 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. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.' alternative_title: - LNCS 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. 2013;8052:273-287. doi:10.1007/978-3-642-40184-8_20 apa: 'Henzinger, T. A., & Otop, J. (2013). From model checking to model measuring. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-40184-8_20' chicago: Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_20. ieee: T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013. ista: Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052, 273–287. mla: Henzinger, Thomas A., and Jan Otop. From Model Checking to Model Measuring. Vol. 8052, Springer, 2013, pp. 273–87, doi:10.1007/978-3-642-40184-8_20. short: T.A. Henzinger, J. Otop, 8052 (2013) 273–287. conference: end_date: 2013-08-30 location: Buenos Aires, Argentina name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:00Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T12:25:26Z day: '01' ddc: - '005' - '000' department: - _id: ToHe doi: 10.1007/978-3-642-40184-8_20 file: - access_level: open_access checksum: 4c04695c4bfdf2119cd4f5d1babc3e8a content_type: application/pdf creator: system date_created: 2018-12-12T10:17:45Z date_updated: 2020-07-14T12:45:38Z file_id: '5301' file_name: IST-2013-129-v1+1_concur.pdf file_size: 378587 relation: main_file file_date_updated: 2020-07-14T12:45:38Z has_accepted_license: '1' intvolume: ' 8052' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 273 - 287 publication_status: published publisher: Springer publist_id: '4599' pubrep_id: '129' quality_controlled: '1' related_material: record: - id: '5417' relation: earlier_version status: public series_title: Lecture Notes in Computer Science status: public title: From model checking to model measuring type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '590' abstract: - lang: eng text: We present two methods of creating two orthogonally-polarized focal points at customizable relative locations. These schemes may be critical for enhancing entanglement sources and other applications. alternative_title: - Optics InfoBase Conference Papers author: - first_name: David full_name: Schmid, David last_name: Schmid - first_name: Ting full_name: Huang, Ting-Yu last_name: Huang - first_name: Radhika full_name: Dirks, Radhika last_name: Dirks - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. Polarization dependent focusing. In: OSA; 2013. doi:10.1364/QIM.2013.W6.23' apa: 'Schmid, D., Huang, T., Dirks, R., Hosten, O., & Kwiat, P. (2013). Polarization dependent focusing. Presented at the QIM: Quantum Information and Measurement, OSA. https://doi.org/10.1364/QIM.2013.W6.23' chicago: Schmid, David, Ting Huang, Radhika Dirks, Onur Hosten, and Paul Kwiat. “Polarization Dependent Focusing.” OSA, 2013. https://doi.org/10.1364/QIM.2013.W6.23. ieee: 'D. Schmid, T. Huang, R. Dirks, O. Hosten, and P. Kwiat, “Polarization dependent focusing,” presented at the QIM: Quantum Information and Measurement, 2013.' ista: 'Schmid D, Huang T, Dirks R, Hosten O, Kwiat P. 2013. Polarization dependent focusing. QIM: Quantum Information and Measurement, Optics InfoBase Conference Papers, .' mla: Schmid, David, et al. Polarization Dependent Focusing. OSA, 2013, doi:10.1364/QIM.2013.W6.23. short: D. Schmid, T. Huang, R. Dirks, O. Hosten, P. Kwiat, in:, OSA, 2013. conference: name: 'QIM: Quantum Information and Measurement' date_created: 2018-12-11T11:47:22Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:05:10Z day: '01' doi: 10.1364/QIM.2013.W6.23 extern: 1 month: '01' publication_status: published publisher: OSA publist_id: '7217' quality_controlled: 0 status: public title: Polarization dependent focusing type: conference year: '2013' ... --- _id: '5920' abstract: - lang: eng text: We study chains of lattice ideals that are invariant under a symmetric group action. In our setting, the ambient rings for these ideals are polynomial rings which are increasing in (Krull) dimension. Thus, these chains will fail to stabilize in the traditional commutative algebra sense. However, we prove a theorem which says that “up to the action of the group”, these chains locally stabilize. We also give an algorithm, which we have implemented in software, for explicitly constructing these stabilization generators for a family of Laurent toric ideals involved in applications to algebraic statistics. We close with several open problems and conjectures arising from our theoretical and computational investigations. article_processing_charge: No article_type: original author: - first_name: Christopher J. full_name: Hillar, Christopher J. last_name: Hillar - first_name: Abraham full_name: Martin del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin del Campo Sanchez citation: ama: Hillar CJ, Martin del Campo Sanchez A. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 2013;50:314-334. doi:10.1016/j.jsc.2012.06.006 apa: Hillar, C. J., & Martin del Campo Sanchez, A. (2013). Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2012.06.006 chicago: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation. Elsevier, 2013. https://doi.org/10.1016/j.jsc.2012.06.006. ieee: C. J. Hillar and A. Martin del Campo Sanchez, “Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals,” Journal of Symbolic Computation, vol. 50. Elsevier, pp. 314–334, 2013. ista: Hillar CJ, Martin del Campo Sanchez A. 2013. Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals. Journal of Symbolic Computation. 50, 314–334. mla: Hillar, Christopher J., and Abraham Martin del Campo Sanchez. “Finiteness Theorems and Algorithms for Permutation Invariant Chains of Laurent Lattice Ideals.” Journal of Symbolic Computation, vol. 50, Elsevier, 2013, pp. 314–34, doi:10.1016/j.jsc.2012.06.006. short: C.J. Hillar, A. Martin del Campo Sanchez, Journal of Symbolic Computation 50 (2013) 314–334. date_created: 2019-02-05T08:48:24Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T08:05:15Z day: '01' doi: 10.1016/j.jsc.2012.06.006 extern: '1' intvolume: ' 50' language: - iso: eng month: '03' oa_version: None page: 314-334 publication: Journal of Symbolic Computation publication_identifier: issn: - 0747-7171 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1016/j.jsc.2015.09.002 status: public title: Finiteness theorems and algorithms for permutation invariant chains of Laurent lattice ideals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2013' ... --- _id: '591' abstract: - lang: eng text: We present two methods for the precise independent focusing of orthogonal linear polarizations of light at arbitrary relative locations. Our first scheme uses a displaced lens in a polarization Sagnac interferometer to provide adjustable longitudinal and lateral focal displacements via simple geometry; the second uses uniaxial crystals to achieve the same effect in a compact collinear setup. We develop the theoretical applications and limitations of our schemes, and provide experimental confirmation of our calculations. author: - first_name: David full_name: Schmid, David last_name: Schmid - first_name: Ting full_name: Huang, Ting-Yu last_name: Huang - first_name: Shiraz full_name: Hazrat, Shiraz last_name: Hazrat - first_name: Radhika full_name: Dirks, Radhika last_name: Dirks - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Stephan full_name: Quint, Stephan last_name: Quint - first_name: Dickson full_name: Thian, Dickson last_name: Thian - first_name: Paul full_name: Kwiat, Paul G last_name: Kwiat citation: ama: Schmid D, Huang T, Hazrat S, et al. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 2013;21(13):15538-15552. doi:10.1364/OE.21.015538 apa: Schmid, D., Huang, T., Hazrat, S., Dirks, R., Hosten, O., Quint, S., … Kwiat, P. (2013). Adjustable and robust methods for polarization-dependent focusing. Optics Express. Optical Society of America. https://doi.org/10.1364/OE.21.015538 chicago: Schmid, David, Ting Huang, Shiraz Hazrat, Radhika Dirks, Onur Hosten, Stephan Quint, Dickson Thian, and Paul Kwiat. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” Optics Express. Optical Society of America, 2013. https://doi.org/10.1364/OE.21.015538. ieee: D. Schmid et al., “Adjustable and robust methods for polarization-dependent focusing,” Optics Express, vol. 21, no. 13. Optical Society of America, pp. 15538–15552, 2013. ista: Schmid D, Huang T, Hazrat S, Dirks R, Hosten O, Quint S, Thian D, Kwiat P. 2013. Adjustable and robust methods for polarization-dependent focusing. Optics Express. 21(13), 15538–15552. mla: Schmid, David, et al. “Adjustable and Robust Methods for Polarization-Dependent Focusing.” Optics Express, vol. 21, no. 13, Optical Society of America, 2013, pp. 15538–52, doi:10.1364/OE.21.015538. short: D. Schmid, T. Huang, S. Hazrat, R. Dirks, O. Hosten, S. Quint, D. Thian, P. Kwiat, Optics Express 21 (2013) 15538–15552. date_created: 2018-12-11T11:47:22Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:05:12Z day: '01' doi: 10.1364/OE.21.015538 extern: 1 intvolume: ' 21' issue: '13' month: '07' page: 15538 - 15552 publication: Optics Express publication_status: published publisher: Optical Society of America publist_id: '7218' quality_controlled: 0 status: public title: Adjustable and robust methods for polarization-dependent focusing type: journal_article volume: 21 year: '2013' ... --- _id: '595' article_processing_charge: No author: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Patrick full_name: Cramer, Patrick last_name: Cramer citation: ama: 'Bernecky C, Cramer P. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 2013;32(6):771-772. doi:10.1038/emboj.2013.36' apa: 'Bernecky, C., & Cramer, P. (2013). Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.36' chicago: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.36.' ieee: 'C. Bernecky and P. Cramer, “Struggling to let go: A non-coding RNA directs its own extension and destruction,” EMBO Journal, vol. 32, no. 6. Wiley-Blackwell, pp. 771–772, 2013.' ista: 'Bernecky C, Cramer P. 2013. Struggling to let go: A non-coding RNA directs its own extension and destruction. EMBO Journal. 32(6), 771–772.' mla: 'Bernecky, Carrie, and Patrick Cramer. “Struggling to Let Go: A Non-Coding RNA Directs Its Own Extension and Destruction.” EMBO Journal, vol. 32, no. 6, Wiley-Blackwell, 2013, pp. 771–72, doi:10.1038/emboj.2013.36.' short: C. Bernecky, P. Cramer, EMBO Journal 32 (2013) 771–772. date_created: 2018-12-11T11:47:23Z date_published: 2013-03-20T00:00:00Z date_updated: 2021-01-12T08:05:20Z day: '20' doi: 10.1038/emboj.2013.36 extern: '1' intvolume: ' 32' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604726/ month: '03' oa: 1 oa_version: None page: 771 - 772 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '7207' status: public title: 'Struggling to let go: A non-coding RNA directs its own extension and destruction' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '6128' abstract: - lang: eng text: Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O2 and CO2. CO2 is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO2 responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing neuron URX inhibits CO2 avoidance. This inhibition can be graded according to O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to modulate CO2 responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans. article_number: e1004011 author: - first_name: Eiji full_name: Kodama-Namba, Eiji last_name: Kodama-Namba - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - first_name: Andrew J. full_name: Bretscher, Andrew J. last_name: Bretscher - first_name: Einav full_name: Gross, Einav last_name: Gross - first_name: K. Emanuel full_name: Busch, K. Emanuel last_name: Busch - 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: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 2013;9(12). doi:10.1371/journal.pgen.1004011 apa: Kodama-Namba, E., Fenk, L. A., Bretscher, A. J., Gross, E., Busch, K. E., & de Bono, M. (2013). Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1004011 chicago: Kodama-Namba, Eiji, Lorenz A. Fenk, Andrew J. Bretscher, Einav Gross, K. Emanuel Busch, and Mario de Bono. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics. Public Library of Science (PLoS), 2013. https://doi.org/10.1371/journal.pgen.1004011. ieee: E. Kodama-Namba, L. A. Fenk, A. J. Bretscher, E. Gross, K. E. Busch, and M. de Bono, “Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans,” PLoS Genetics, vol. 9, no. 12. Public Library of Science (PLoS), 2013. ista: Kodama-Namba E, Fenk LA, Bretscher AJ, Gross E, Busch KE, de Bono M. 2013. Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans. PLoS Genetics. 9(12), e1004011. mla: Kodama-Namba, Eiji, et al. “Cross-Modulation of Homeostatic Responses to Temperature, Oxygen and Carbon Dioxide in C. Elegans.” PLoS Genetics, vol. 9, no. 12, e1004011, Public Library of Science (PLoS), 2013, doi:10.1371/journal.pgen.1004011. short: E. Kodama-Namba, L.A. Fenk, A.J. Bretscher, E. Gross, K.E. Busch, M. de Bono, PLoS Genetics 9 (2013). date_created: 2019-03-19T14:58:51Z date_published: 2013-12-19T00:00:00Z date_updated: 2021-01-12T08:06:15Z day: '19' ddc: - '570' doi: 10.1371/journal.pgen.1004011 extern: '1' external_id: pmid: - '24385919' file: - access_level: open_access checksum: 299b6321be79931c7c17c5db6e69c711 content_type: application/pdf creator: kschuh date_created: 2019-03-19T15:14:51Z date_updated: 2020-07-14T12:47:20Z file_id: '6129' file_name: 2013_PLOS_Kodama-Namba.PDF file_size: 4499039 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 9' issue: '12' language: - iso: eng month: '12' 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: Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans 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: 9 year: '2013' ... --- _id: '6130' abstract: - lang: eng text: 'Cas9 is an RNA-guided double-stranded DNA nuclease that participates in clustered regularly interspaced short palindromic repeats (CRISPR)-mediated adaptive immunity in prokaryotes. CRISPR–Cas9 has recently been used to generate insertion and deletion mutations in Caenorhabditis elegans, but not to create tailored changes (knock-ins). We show that the CRISPR–CRISPR-associated (Cas) system can be adapted for efficient and precise editing of the C. elegans genome. The targeted double-strand breaks generated by CRISPR are substrates for transgene-instructed gene conversion. This allows customized changes in the C. elegans genome by homologous recombination: sequences contained in the repair template (the transgene) are copied by gene conversion into the genome. The possibility to edit the C. elegans genome at selected locations will facilitate the systematic study of gene function in this widely used model organism.' article_number: e193 author: - first_name: Changchun full_name: Chen, Changchun last_name: Chen - first_name: Lorenz A. full_name: Fenk, Lorenz A. last_name: Fenk - 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, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 2013;41(20). doi:10.1093/nar/gkt805 apa: Chen, C., Fenk, L. A., & de Bono, M. (2013). Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkt805 chicago: Chen, Changchun, Lorenz A. Fenk, and Mario de Bono. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research. Oxford University Press, 2013. https://doi.org/10.1093/nar/gkt805. ieee: C. Chen, L. A. Fenk, and M. de Bono, “Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination,” Nucleic Acids Research, vol. 41, no. 20. Oxford University Press, 2013. ista: Chen C, Fenk LA, de Bono M. 2013. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Research. 41(20), e193. mla: Chen, Changchun, et al. “Efficient Genome Editing in Caenorhabditis Elegans by CRISPR-Targeted Homologous Recombination.” Nucleic Acids Research, vol. 41, no. 20, e193, Oxford University Press, 2013, doi:10.1093/nar/gkt805. short: C. Chen, L.A. Fenk, M. de Bono, Nucleic Acids Research 41 (2013). date_created: 2019-03-19T15:17:40Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '01' ddc: - '570' doi: 10.1093/nar/gkt805 extern: '1' external_id: pmid: - '24013562' file: - access_level: open_access checksum: 0f1f127cefd043cb922b292e1cd16f02 content_type: application/pdf creator: kschuh date_created: 2019-03-19T15:25:42Z date_updated: 2020-07-14T12:47:20Z file_id: '6131' file_name: 2013_OUP_Chen.pdf file_size: 340225 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 41' issue: '20' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nucleic Acids Research publication_identifier: issn: - 1362-4962 - 0305-1048 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination 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: 41 year: '2013' ... --- _id: '6133' abstract: - lang: eng text: cGMP signaling is widespread in the nervous system. However, it has proved difficult to visualize and genetically probe endogenously evoked cGMP dynamics in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical O2-binding soluble guanylate cyclase and that is sustained until oxygen levels fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2) and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation following a rise in O2, apparently by keeping in check gating of cGMP channels and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible when the same neuron in an individual animal is stimulated repeatedly, suggesting that cGMP transduction has high intrinsic reliability. However, responses vary substantially across individuals, despite animals being genetically identical and similarly reared. This variability may reflect stochastic differences in expression of cGMP signaling components. Our work provides in vivo insights into the architecture of neuronal cGMP signaling. author: - first_name: A. full_name: Couto, A. last_name: Couto - first_name: S. full_name: Oda, S. last_name: Oda - first_name: V. O. full_name: Nikolaev, V. O. last_name: Nikolaev - first_name: Z. full_name: Soltesz, Z. last_name: Soltesz - 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: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 2013;110(35):E3301-E3310. doi:10.1073/pnas.1217428110 apa: Couto, A., Oda, S., Nikolaev, V. O., Soltesz, Z., & de Bono, M. (2013). In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1217428110 chicago: Couto, A., S. Oda, V. O. Nikolaev, Z. Soltesz, and Mario de Bono. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217428110. ieee: A. Couto, S. Oda, V. O. Nikolaev, Z. Soltesz, and M. de Bono, “In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor,” Proceedings of the National Academy of Sciences, vol. 110, no. 35. Proceedings of the National Academy of Sciences, pp. E3301–E3310, 2013. ista: Couto A, Oda S, Nikolaev VO, Soltesz Z, de Bono M. 2013. In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor. Proceedings of the National Academy of Sciences. 110(35), E3301–E3310. mla: Couto, A., et al. “In Vivo Genetic Dissection of O2-Evoked CGMP Dynamics in a Caenorhabditis Elegans Gas Sensor.” Proceedings of the National Academy of Sciences, vol. 110, no. 35, Proceedings of the National Academy of Sciences, 2013, pp. E3301–10, doi:10.1073/pnas.1217428110. short: A. Couto, S. Oda, V.O. Nikolaev, Z. Soltesz, M. de Bono, Proceedings of the National Academy of Sciences 110 (2013) E3301–E3310. date_created: 2019-03-20T14:05:06Z date_published: 2013-08-27T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '27' ddc: - '570' doi: 10.1073/pnas.1217428110 extern: '1' external_id: pmid: - '23940325' file: - access_level: open_access checksum: 3ee28a694f74a49f0d098970ae391a91 content_type: application/pdf creator: kschuh date_created: 2019-03-20T14:07:53Z date_updated: 2020-07-14T12:47:20Z file_id: '6134' file_name: 2013_PNAS_Couto.pdf file_size: 2198763 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 110' issue: '35' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: E3301-E3310 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' status: public title: In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '6135' abstract: - lang: eng text: Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery. author: - first_name: Miriam full_name: Rodriguez, Miriam last_name: Rodriguez - first_name: L. Basten full_name: Snoek, L. Basten last_name: Snoek - 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: Jan E. full_name: Kammenga, Jan E. last_name: Kammenga citation: ama: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 2013;29(6):367-374. doi:10.1016/j.tig.2013.01.010' apa: 'Rodriguez, M., Snoek, L. B., de Bono, M., & Kammenga, J. E. (2013). Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2013.01.010' chicago: 'Rodriguez, Miriam, L. Basten Snoek, Mario de Bono, and Jan E. Kammenga. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics. Elsevier, 2013. https://doi.org/10.1016/j.tig.2013.01.010.' ieee: 'M. Rodriguez, L. B. Snoek, M. de Bono, and J. E. Kammenga, “Worms under stress: C. elegans stress response and its relevance to complex human disease and aging,” Trends in Genetics, vol. 29, no. 6. Elsevier, pp. 367–374, 2013.' ista: 'Rodriguez M, Snoek LB, de Bono M, Kammenga JE. 2013. Worms under stress: C. elegans stress response and its relevance to complex human disease and aging. Trends in Genetics. 29(6), 367–374.' mla: 'Rodriguez, Miriam, et al. “Worms under Stress: C. Elegans Stress Response and Its Relevance to Complex Human Disease and Aging.” Trends in Genetics, vol. 29, no. 6, Elsevier, 2013, pp. 367–74, doi:10.1016/j.tig.2013.01.010.' short: M. Rodriguez, L.B. Snoek, M. de Bono, J.E. Kammenga, Trends in Genetics 29 (2013) 367–374. date_created: 2019-03-20T14:17:42Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T08:06:17Z day: '01' doi: 10.1016/j.tig.2013.01.010 extern: '1' intvolume: ' 29' issue: '6' language: - iso: eng month: '06' oa_version: None page: 367-374 publication: Trends in Genetics publication_identifier: issn: - 0168-9525 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Worms under stress: C. elegans stress response and its relevance to complex human disease and aging' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2013' ... --- _id: '6132' author: - 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: W.R. full_name: Schafer, W.R. last_name: Schafer - first_name: A. full_name: Gottschalk, A. last_name: Gottschalk citation: ama: 'de Bono M, Schafer WR, Gottschalk A. Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Hegemann P, Sigrist S, eds. Optogenetics. Walter de Gruyter; 2013:61-78.' apa: de Bono, M., Schafer, W. R., & Gottschalk, A. (2013). Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In P. Hegemann & S. Sigrist (Eds.), Optogenetics (pp. 61–78). Walter de Gruyter. chicago: Bono, Mario de, W.R. Schafer, and A. Gottschalk. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” In Optogenetics, edited by Peter Hegemann and Stephan Sigrist, 61–78. Walter de Gruyter, 2013. ieee: M. de Bono, W. R. Schafer, and A. Gottschalk, “Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans,” in Optogenetics, P. Hegemann and S. Sigrist, Eds. Walter de Gruyter, 2013, pp. 61–78. ista: 'de Bono M, Schafer WR, Gottschalk A. 2013.Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans. In: Optogenetics. , 61–78.' mla: de Bono, Mario, et al. “Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans.” Optogenetics, edited by Peter Hegemann and Stephan Sigrist, Walter de Gruyter, 2013, pp. 61–78. short: M. de Bono, W.R. Schafer, A. Gottschalk, in:, P. Hegemann, S. Sigrist (Eds.), Optogenetics, Walter de Gruyter, 2013, pp. 61–78. date_created: 2019-03-20T13:54:05Z date_published: 2013-08-28T00:00:00Z date_updated: 2021-01-12T08:06:16Z day: '28' editor: - first_name: Peter full_name: Hegemann, Peter last_name: Hegemann - first_name: Stephan full_name: Sigrist, Stephan last_name: Sigrist extern: '1' language: - iso: eng month: '08' oa_version: None page: 61-78 publication: Optogenetics publication_identifier: isbn: - 9783110270723; 9783110270716 publication_status: published publisher: Walter de Gruyter quality_controlled: '1' status: public title: Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '6370' abstract: - lang: eng text: 'The molecular and supramolecular origins of the superior nonlinear optical (NLO) properties observed in the organic phenolic triene material, OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile), are presented. The molecular charge-transfer distribution is topographically mapped, demonstrating that a uniformly delocalized passive electronic medium facilitates the charge-transfer between the phenolic electron donor and the cyano electron acceptors which lie at opposite ends of the molecule. Its ability to act as a “push–pull” π-conjugated molecule is quantified, relative to similar materials, by supporting empirical calculations; these include bond-length alternation and harmonic-oscillator stabilization energy (HOSE) tests. Such tests, together with frontier molecular orbital considerations, reveal that OH1 can exist readily in its aromatic (neutral) or quinoidal (charge-separated) state, thereby overcoming the “nonlinearity-thermal stability trade-off”. The HOSE calculation also reveals a correlation between the quinoidal resonance contribution to the overall structure of OH1 and the UV–vis absorption peak wavelength in the wider family of configurationally locked polyene framework materials. Solid-state tensorial coefficients of the molecular dipole, polarizability, and the first hyperpolarizability for OH1 are derived from the first-, second-, and third-order electronic moments of the experimental charge-density distribution. The overall solid-state molecular dipole moment is compared with those from gas-phase calculations, revealing that crystal field effects are very significant in OH1. The solid-state hyperpolarizability derived from this charge-density study affords good agreement with gas-phase calculations as well as optical measurements based on hyper-Rayleigh scattering (HRS) and electric-field-induced second harmonic (EFISH) generation. This lends support to the further use of charge-density studies to calculate solid-state hyperpolarizability coefficients in other organic NLO materials. Finally, this charge-density study is also employed to provide an advanced classification of hydrogen bonds in OH1, which requires more stringent criteria than those from conventional structure analysis. As a result, only the strongest OH···NC interaction is so classified as a true hydrogen bond. Indeed, it is this electrostatic interaction that influences the molecular charge transfer: the other four, weaker, nonbonded contacts nonetheless affect the crystal packing. Overall, the establishment of these structure–property relationships lays a blueprint for designing further, more NLO efficient, materials in this industrially leading organic family of compounds.' author: - first_name: Tze-Chia full_name: Lin, Tze-Chia last_name: Lin - first_name: Jacqueline M. full_name: Cole, Jacqueline M. last_name: Cole - 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: Alison J. full_name: Edwards, Alison J. last_name: Edwards - first_name: Ross O. full_name: Piltz, Ross O. last_name: Piltz - first_name: Javier full_name: Pérez-Moreno, Javier last_name: Pérez-Moreno - first_name: Ji-Youn full_name: Seo, Ji-Youn last_name: Seo - first_name: Seung-Chul full_name: Lee, Seung-Chul last_name: Lee - first_name: Koen full_name: Clays, Koen last_name: Clays - first_name: O-Pil full_name: Kwon, O-Pil last_name: Kwon citation: ama: 'Lin T-C, Cole JM, Higginbotham AP, et al. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 2013;117(18):9416-9430. doi:10.1021/jp400648q' apa: 'Lin, T.-C., Cole, J. M., Higginbotham, A. P., Edwards, A. J., Piltz, R. O., Pérez-Moreno, J., … Kwon, O.-P. (2013). Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. American Chemical Society (ACS). https://doi.org/10.1021/jp400648q' chicago: 'Lin, Tze-Chia, Jacqueline M. Cole, Andrew P Higginbotham, Alison J. Edwards, Ross O. Piltz, Javier Pérez-Moreno, Ji-Youn Seo, Seung-Chul Lee, Koen Clays, and O-Pil Kwon. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry C. American Chemical Society (ACS), 2013. https://doi.org/10.1021/jp400648q.' ieee: 'T.-C. Lin et al., “Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations,” The Journal of Physical Chemistry C, vol. 117, no. 18. American Chemical Society (ACS), pp. 9416–9430, 2013.' ista: 'Lin T-C, Cole JM, Higginbotham AP, Edwards AJ, Piltz RO, Pérez-Moreno J, Seo J-Y, Lee S-C, Clays K, Kwon O-P. 2013. Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations. The Journal of Physical Chemistry C. 117(18), 9416–9430.' mla: 'Lin, Tze-Chia, et al. “Molecular Origins of the High-Performance Nonlinear Optical Susceptibility in a Phenolic Polyene Chromophore: Electron Density Distributions, Hydrogen Bonding, and Ab Initio Calculations.” The Journal of Physical Chemistry C, vol. 117, no. 18, American Chemical Society (ACS), 2013, pp. 9416–30, doi:10.1021/jp400648q.' short: T.-C. Lin, J.M. Cole, A.P. Higginbotham, A.J. Edwards, R.O. Piltz, J. Pérez-Moreno, J.-Y. Seo, S.-C. Lee, K. Clays, O.-P. Kwon, The Journal of Physical Chemistry C 117 (2013) 9416–9430. date_created: 2019-05-03T09:40:31Z date_published: 2013-05-09T00:00:00Z date_updated: 2021-01-12T08:07:17Z day: '09' doi: 10.1021/jp400648q extern: '1' intvolume: ' 117' issue: '18' language: - iso: eng month: '05' oa_version: None page: 9416-9430 publication: The Journal of Physical Chemistry C publication_identifier: issn: - 1932-7447 - 1932-7455 publication_status: published publisher: American Chemical Society (ACS) quality_controlled: '1' status: public title: 'Molecular origins of the high-performance nonlinear optical susceptibility in a phenolic polyene chromophore: Electron density distributions, hydrogen bonding, and ab initio calculations' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2013' ... --- _id: '6440' abstract: - lang: eng text: In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations. We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance. In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations. 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: Hannes full_name: Payer, Hannes last_name: Payer - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: Henzinger TA, Payer H, Sezgin A. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria; 2013. doi:10.15479/AT:IST-2013-124-v1-1 apa: Henzinger, T. A., Payer, H., & Sezgin, A. (2013). Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria. https://doi.org/10.15479/AT:IST-2013-124-v1-1 chicago: Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-124-v1-1. ieee: T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation to achieve scalable lock-free FIFO queues . IST Austria, 2013. ista: Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p. mla: Henzinger, Thomas A., et al. Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria, 2013, doi:10.15479/AT:IST-2013-124-v1-1. short: T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013. date_created: 2019-05-13T14:13:27Z date_published: 2013-06-13T00:00:00Z date_updated: 2020-07-14T23:06:19Z day: '13' ddc: - '000' - '005' department: - _id: ToHe doi: 10.15479/AT:IST-2013-124-v1-1 file: - access_level: open_access checksum: a219ba4eada6cd62befed52262ee15d4 content_type: application/pdf creator: dernst date_created: 2019-05-13T14:11:39Z date_updated: 2020-07-14T12:47:30Z file_id: '6441' file_name: 2013_TechRep_Henzinger.pdf file_size: 549684 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '23' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '124' status: public title: 'Replacing competition with cooperation to achieve scalable lock-free FIFO queues ' type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '6768' abstract: - lang: eng text: The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme. article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: Mondelli M. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 2013;3:68-111. doi:10.5201/ipol.2013.53 apa: Mondelli, M. (2013). A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. Image Processing On Line. https://doi.org/10.5201/ipol.2013.53 chicago: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line. Image Processing On Line, 2013. https://doi.org/10.5201/ipol.2013.53. ieee: M. Mondelli, “A finite difference scheme for the stack filter simulating the MCM,” Image Processing On Line, vol. 3. Image Processing On Line, pp. 68–111, 2013. ista: Mondelli M. 2013. A finite difference scheme for the stack filter simulating the MCM. Image Processing On Line. 3, 68–111. mla: Mondelli, Marco. “A Finite Difference Scheme for the Stack Filter Simulating the MCM.” Image Processing On Line, vol. 3, Image Processing On Line, 2013, pp. 68–111, doi:10.5201/ipol.2013.53. short: M. Mondelli, Image Processing On Line 3 (2013) 68–111. date_created: 2019-08-05T12:30:38Z date_published: 2013-07-11T00:00:00Z date_updated: 2021-01-12T08:08:56Z day: '11' ddc: - '510' doi: 10.5201/ipol.2013.53 extern: '1' file: - access_level: open_access checksum: 83b7d429bc248c6c461229d3504fb139 content_type: application/pdf creator: dernst date_created: 2019-08-05T12:33:40Z date_updated: 2020-07-14T12:47:40Z file_id: '6769' file_name: 2013_IPOL_Mondelli.pdf file_size: 4306158 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 68-111 publication: Image Processing On Line publication_identifier: issn: - 2105-1232 publication_status: published publisher: Image Processing On Line quality_controlled: '1' status: public title: A finite difference scheme for the stack filter simulating the MCM tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2329' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity 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: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. 2013;8052:500-515. doi:10.1007/978-3-642-40184-8_35 apa: 'Chatterjee, K., & Velner, Y. (2013). Hyperplane separation technique for multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentinia: Springer. https://doi.org/10.1007/978-3-642-40184-8_35' chicago: Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40184-8_35. ieee: K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013. ista: Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515. mla: Chatterjee, Krishnendu, and Yaron Velner. Hyperplane Separation Technique for Multidimensional Mean-Payoff Games. Vol. 8052, Springer, 2013, pp. 500–15, doi:10.1007/978-3-642-40184-8_35. short: K. Chatterjee, Y. Velner, 8052 (2013) 500–515. conference: end_date: 2013-08-30 location: Buenos Aires, Argentinia name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:01Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T13:00:42Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-40184-8_35 ec_funded: 1 external_id: arxiv: - '1210.3141' intvolume: ' 8052' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1210.3141 month: '08' oa: 1 oa_version: Preprint page: 500 - 515 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: '4597' quality_controlled: '1' related_material: record: - id: '717' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Hyperplane separation technique for multidimensional mean-payoff games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '7306' abstract: - lang: eng text: Rechargeable lithium–air (O2) batteries are receiving intense interest because their high theoretical specific energy exceeds that of lithium-ion batteries. If the Li–O2 battery is ever to succeed, highly reversible formation/decomposition of Li2O2 must take place at the cathode on cycling. However, carbon, used ubiquitously as the basis of the cathode, decomposes during Li2O2 oxidation on charge and actively promotes electrolyte decomposition on cycling. Replacing carbon with a nanoporous gold cathode, when in contact with a dimethyl sulphoxide-based electrolyte, does seem to demonstrate better stability. However, nanoporous gold is not a suitable cathode; its high mass destroys the key advantage of Li–O2 over Li ion (specific energy), it is too expensive and too difficult to fabricate. Identifying a suitable cathode material for the Li–O2 cell is one of the greatest challenges at present. Here we show that a TiC-based cathode reduces greatly side reactions (arising from the electrolyte and electrode degradation) compared with carbon and exhibits better reversible formation/decomposition of Li2O2 even than nanoporous gold (>98% capacity retention after 100 cycles, compared with 95% for nanoporous gold); it is also four times lighter, of lower cost and easier to fabricate. The stability may originate from the presence of TiO2 (along with some TiOC) on the surface of TiC. In contrast to carbon or nanoporous gold, TiC seems to represent a more viable, stable, cathode for aprotic Li–O2 cells. article_processing_charge: No article_type: original author: - first_name: Muhammed M. full_name: Ottakam Thotiyl, Muhammed M. last_name: Ottakam Thotiyl - 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: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Yuhui full_name: Chen, Yuhui last_name: Chen - first_name: Zheng full_name: Liu, Zheng last_name: Liu - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 2013;12(11):1050-1056. doi:10.1038/nmat3737 apa: Ottakam Thotiyl, M. M., Freunberger, S. A., Peng, Z., Chen, Y., Liu, Z., & Bruce, P. G. (2013). A stable cathode for the aprotic Li–O2 battery. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat3737 chicago: Ottakam Thotiyl, Muhammed M., Stefan Alexander Freunberger, Zhangquan Peng, Yuhui Chen, Zheng Liu, and Peter G. Bruce. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials. Springer Nature, 2013. https://doi.org/10.1038/nmat3737. ieee: M. M. Ottakam Thotiyl, S. A. Freunberger, Z. Peng, Y. Chen, Z. Liu, and P. G. Bruce, “A stable cathode for the aprotic Li–O2 battery,” Nature Materials, vol. 12, no. 11. Springer Nature, pp. 1050–1056, 2013. ista: Ottakam Thotiyl MM, Freunberger SA, Peng Z, Chen Y, Liu Z, Bruce PG. 2013. A stable cathode for the aprotic Li–O2 battery. Nature Materials. 12(11), 1050–1056. mla: Ottakam Thotiyl, Muhammed M., et al. “A Stable Cathode for the Aprotic Li–O2 Battery.” Nature Materials, vol. 12, no. 11, Springer Nature, 2013, pp. 1050–56, doi:10.1038/nmat3737. short: M.M. Ottakam Thotiyl, S.A. Freunberger, Z. Peng, Y. Chen, Z. Liu, P.G. Bruce, Nature Materials 12 (2013) 1050–1056. date_created: 2020-01-15T12:18:29Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:12:55Z day: '01' doi: 10.1038/nmat3737 extern: '1' intvolume: ' 12' issue: '11' language: - iso: eng month: '09' oa_version: None page: 1050-1056 publication: Nature Materials publication_identifier: issn: - 1476-1122 - 1476-4660 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: A stable cathode for the aprotic Li–O2 battery type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2013' ... --- _id: '7307' abstract: - lang: eng text: The non-aqueous Li–air (O2) battery is receiving intense interest because its theoretical specific energy exceeds that of Li-ion batteries. Recharging the Li–O2 battery depends on oxidizing solid lithium peroxide (Li2O2), which is formed on discharge within the porous cathode. However, transporting charge between Li2O2 particles and the solid electrode surface is at best very difficult and leads to voltage polarization on charging, even at modest rates. This is a significant problem facing the non-aqueous Li–O2 battery. Here we show that incorporation of a redox mediator, tetrathiafulvalene (TTF), enables recharging at rates that are impossible for the cell in the absence of the mediator. On charging, TTF is oxidized to TTF+ at the cathode surface; TTF+ in turn oxidizes the solid Li2O2, which results in the regeneration of TTF. The mediator acts as an electron–hole transfer agent that permits efficient oxidation of solid Li2O2. The cell with the mediator demonstrated 100 charge/discharge cycles. article_processing_charge: No article_type: original author: - 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: Zhangquan full_name: Peng, Zhangquan last_name: Peng - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce citation: ama: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 2013;5(6):489-494. doi:10.1038/nchem.1646 apa: Chen, Y., Freunberger, S. A., Peng, Z., Fontaine, O., & Bruce, P. G. (2013). Charging a Li–O2 battery using a redox mediator. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.1646 chicago: Chen, Yuhui, Stefan Alexander Freunberger, Zhangquan Peng, Olivier Fontaine, and Peter G. Bruce. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry. Springer Nature, 2013. https://doi.org/10.1038/nchem.1646. ieee: Y. Chen, S. A. Freunberger, Z. Peng, O. Fontaine, and P. G. Bruce, “Charging a Li–O2 battery using a redox mediator,” Nature Chemistry, vol. 5, no. 6. Springer Nature, pp. 489–494, 2013. ista: Chen Y, Freunberger SA, Peng Z, Fontaine O, Bruce PG. 2013. Charging a Li–O2 battery using a redox mediator. Nature Chemistry. 5(6), 489–494. mla: Chen, Yuhui, et al. “Charging a Li–O2 Battery Using a Redox Mediator.” Nature Chemistry, vol. 5, no. 6, Springer Nature, 2013, pp. 489–94, doi:10.1038/nchem.1646. short: Y. Chen, S.A. Freunberger, Z. Peng, O. Fontaine, P.G. Bruce, Nature Chemistry 5 (2013) 489–494. date_created: 2020-01-15T12:18:43Z date_published: 2013-05-12T00:00:00Z date_updated: 2021-01-12T08:12:56Z day: '12' doi: 10.1038/nchem.1646 extern: '1' intvolume: ' 5' issue: '6' language: - iso: eng month: '05' oa_version: None page: 489-494 publication: Nature Chemistry publication_identifier: issn: - 1755-4330 - 1755-4349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Charging a Li–O2 battery using a redox mediator type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2013' ... --- _id: '7596' abstract: - lang: eng text: Casein kinase1 (CK1) plays crucial roles in regulating growth and development via phosphorylating various substrates throughout the eukaryote kingdom. Blue light is crucial for normal growth of both plants and animals, and blue light receptor cryptochrome2 (CRY2) undergoes blue light–dependent phosphorylation and degradation in planta. To study the function of plant CK1s, systematic genetic analysis showed that deficiency of two paralogous Arabidopsis thaliana CK1s, CK1.3 and CK1.4, caused shortened hypocotyls, especially under blue light, while overexpression of either CK1.3 or CK1.4 resulted in the insensitive response to blue light and delayed flowering under long-day conditions. CK1.3 or CK1.4 act dependently on CRY2, and overexpression of CK1.3 or CK1.4 significantly suppresses the hypersensitive response to blue light by CRY2 overexpression. Biochemical studies showed that CK1.3 and CK1.4 directly phosphorylate CRY2 at Ser-587 and Thr-603 in vitro and negatively regulate CRY2 stability in planta, which are stimulated by blue light, further confirming the crucial roles of CK1.3 and CK1.4 in blue light responses through phosphorylating CRY2. Interestingly, expression of CK1.3 and CK1.4 is stimulated by blue light and feedback regulated by CRY2-mediated signaling. These results provide direct evidence for CRY2 phosphorylation and informative clues on the mechanisms of CRY2-mediated light responses. 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: C. full_name: Dai, C. last_name: Dai - first_name: H.-T. full_name: Liu, H.-T. last_name: Liu - first_name: H.-W. full_name: Xue, H.-W. last_name: Xue citation: ama: Tan S, Dai C, Liu H-T, Xue H-W. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 2013;25(7):2618-2632. doi:10.1105/tpc.113.114322 apa: Tan, S., Dai, C., Liu, H.-T., & Xue, H.-W. (2013). Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.114322 chicago: Tan, Shutang, C. Dai, H.-T. Liu, and H.-W. Xue. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114322. ieee: S. Tan, C. Dai, H.-T. Liu, and H.-W. Xue, “Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling,” The Plant Cell, vol. 25, no. 7. American Society of Plant Biologists, pp. 2618–2632, 2013. ista: Tan S, Dai C, Liu H-T, Xue H-W. 2013. Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling. The Plant Cell. 25(7), 2618–2632. mla: Tan, Shutang, et al. “Arabidopsis Casein Kinase1 Proteins CK1.3 and CK1.4 Phosphorylate Cryptochrome2 to Regulate Blue Light Signaling.” The Plant Cell, vol. 25, no. 7, American Society of Plant Biologists, 2013, pp. 2618–32, doi:10.1105/tpc.113.114322. short: S. Tan, C. Dai, H.-T. Liu, H.-W. Xue, The Plant Cell 25 (2013) 2618–2632. date_created: 2020-03-21T16:06:55Z date_published: 2013-08-26T00:00:00Z date_updated: 2021-01-12T08:14:24Z day: '26' doi: 10.1105/tpc.113.114322 extern: '1' external_id: pmid: - '23897926' intvolume: ' 25' issue: '7' language: - iso: eng month: '08' oa_version: None page: 2618-2632 pmid: 1 publication: The Plant Cell publication_identifier: issn: - 1040-4651 - 1532-298X publication_status: published publisher: American Society of Plant Biologists quality_controlled: '1' status: public title: Arabidopsis casein kinase1 proteins CK1.3 and CK1.4 phosphorylate cryptochrome2 to regulate blue light signaling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2013' ... --- _id: '7595' abstract: - lang: eng text: Inositol 1,3,4-trisphosphate 5/6 kinase (ITPK) phosphorylates inositol 1,3,4-trisphosphate to form inositol 1,3,4,5-tetrakisphosphate and inositol 1,3,4,6-tetrakisphosphate which can be finally transferred to inositol hexaphosphate (IP6) and play important roles during plant growth and development. There are 4 putative ITPK members in Arabidopsis. Expression pattern analysis showed that ITPK2 is constitutively expressed in various tissues. A T-DNA knockout mutant of ITPK2 was identified and scanning electron microscopy (SEM) analysis showed that the epidermis structure of seed coat was irregularly formed in seeds of itpk2-1 mutant, resulting in the increased permeability of seed coat to tetrazolium salts. Further analysis by gas chromatography coupled with mass spectrometry of lipid polyester monomers in cell wall confirmed a dramatic decrease in composition of suberin and cutin, which relate to the permeability of seed coat and the formation of which is accompanied with seed coat development. These results indicate that ITPK2 plays an essential role in seed coat development and lipid polyester barrier formation. article_processing_charge: No article_type: original author: - first_name: Yong full_name: Tang, Yong last_name: Tang - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Hongwei full_name: Xue, Hongwei last_name: Xue citation: ama: Tang Y, Tan S, Xue H. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 2013;45(7):549-560. doi:10.1093/abbs/gmt039 apa: Tang, Y., Tan, S., & Xue, H. (2013). Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. Oxford University Press. https://doi.org/10.1093/abbs/gmt039 chicago: Tang, Yong, Shutang Tan, and Hongwei Xue. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica. Oxford University Press, 2013. https://doi.org/10.1093/abbs/gmt039. ieee: Y. Tang, S. Tan, and H. Xue, “Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development,” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7. Oxford University Press, pp. 549–560, 2013. ista: Tang Y, Tan S, Xue H. 2013. Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development. Acta Biochimica et Biophysica Sinica. 45(7), 549–560. mla: Tang, Yong, et al. “Arabidopsis Inositol 1,3,4-Trisphosphate 5/6 Kinase 2 Is Required for Seed Coat Development.” Acta Biochimica et Biophysica Sinica, vol. 45, no. 7, Oxford University Press, 2013, pp. 549–60, doi:10.1093/abbs/gmt039. short: Y. Tang, S. Tan, H. Xue, Acta Biochimica et Biophysica Sinica 45 (2013) 549–560. date_created: 2020-03-21T16:06:36Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T08:14:23Z day: '01' doi: 10.1093/abbs/gmt039 extern: '1' external_id: pmid: - '23595027' intvolume: ' 45' issue: '7' language: - iso: eng month: '07' oa_version: None page: 549-560 pmid: 1 publication: Acta Biochimica et Biophysica Sinica publication_identifier: issn: - 1745-7270 - 1672-9145 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Arabidopsis inositol 1,3,4-trisphosphate 5/6 kinase 2 is required for seed coat development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2013' ... --- _id: '765' abstract: - lang: eng text: Renaming is a classic distributed coordination task in which a set of processes must pick distinct identifiers from a small namespace. In this paper, we consider the time complexity of this problem when the namespace is linear in the number of participants, a variant known as loose renaming. We give a non-adaptive algorithm with O(log log n) (individual) step complexity, where n is a known upper bound on contention, and an adaptive algorithm with step complexity O((log log k)2), where k is the actual contention in the execution. We also present a variant of the adaptive algorithm which requires O(k log log k) total process steps. All upper bounds hold with high probability against a strong adaptive adversary. We complement the algorithms with an ω(log log n) expected time lower bound on the complexity of randomized renaming using test-and-set operations and linear space. The result is based on a new coupling technique, and is the first to apply to non-adaptive randomized renaming. Since our algorithms use O(n) test-and-set objects, our results provide matching bounds on the cost of loose renaming in this setting. acknowledgement: "Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant\r\nER26116/DE-SC0008923, \ and by grants from the Oracle\r\nand Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nGeorge Giakkoupis - This work was funded in part by INRIA Associate Team\r\nRADCON, and ERC Starting Grant GOSSPLE 204742.\r\nPhilipp Woelfel - This research was undertaken, in part, thanks to funding\r\nfrom the Canada Research Chairs program and the HP Labs\r\nInnovation Research Program." 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: George full_name: Giakkoupis, George last_name: Giakkoupis - first_name: Philipp full_name: Woelfel, Philipp last_name: Woelfel citation: ama: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. Randomized loose renaming in O(loglogn) time. In: ACM; 2013:200-209. doi:10.1145/2484239.2484240' apa: 'Alistarh, D.-A., Aspnes, J., Giakkoupis, G., & Woelfel, P. (2013). Randomized loose renaming in O(loglogn) time (pp. 200–209). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2484239.2484240' chicago: Alistarh, Dan-Adrian, James Aspnes, George Giakkoupis, and Philipp Woelfel. “Randomized Loose Renaming in O(Loglogn) Time,” 200–209. ACM, 2013. https://doi.org/10.1145/2484239.2484240. ieee: 'D.-A. Alistarh, J. Aspnes, G. Giakkoupis, and P. Woelfel, “Randomized loose renaming in O(loglogn) time,” presented at the PODC: Principles of Distributed Computing, 2013, pp. 200–209.' ista: 'Alistarh D-A, Aspnes J, Giakkoupis G, Woelfel P. 2013. Randomized loose renaming in O(loglogn) time. PODC: Principles of Distributed Computing, 200–209.' mla: Alistarh, Dan-Adrian, et al. Randomized Loose Renaming in O(Loglogn) Time. ACM, 2013, pp. 200–09, doi:10.1145/2484239.2484240. short: D.-A. Alistarh, J. Aspnes, G. Giakkoupis, P. Woelfel, in:, ACM, 2013, pp. 200–209. conference: name: 'PODC: Principles of Distributed Computing' date_created: 2018-12-11T11:48:23Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-23T13:13:14Z day: '01' doi: 10.1145/2484239.2484240 extern: '1' language: - iso: eng month: '01' oa_version: None page: 200 - 209 publication_status: published publisher: ACM publist_id: '6889' status: public title: Randomized loose renaming in O(loglogn) time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '7745' abstract: - lang: eng text: The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems. 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: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Isabelle full_name: DeCauwer, Isabelle last_name: DeCauwer - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 2013;22(15):3963-3980. doi:10.1111/mec.12375 apa: Robinson, M. R., Santure, A. W., DeCauwer, I., Sheldon, B. C., & Slate, J. (2013). Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12375 chicago: Robinson, Matthew Richard, Anna W. Santure, Isabelle DeCauwer, Ben C. Sheldon, and Jon Slate. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12375. ieee: M. R. Robinson, A. W. Santure, I. DeCauwer, B. C. Sheldon, and J. Slate, “Partitioning of genetic variation across the genome using multimarker methods in a wild bird population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3963–3980, 2013. ista: Robinson MR, Santure AW, DeCauwer I, Sheldon BC, Slate J. 2013. Partitioning of genetic variation across the genome using multimarker methods in a wild bird population. Molecular Ecology. 22(15), 3963–3980. mla: Robinson, Matthew Richard, et al. “Partitioning of Genetic Variation across the Genome Using Multimarker Methods in a Wild Bird Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3963–80, doi:10.1111/mec.12375. short: M.R. Robinson, A.W. Santure, I. DeCauwer, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3963–3980. date_created: 2020-04-30T11:00:15Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:15:14Z day: '01' doi: 10.1111/mec.12375 extern: '1' intvolume: ' 22' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3963-3980 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '7746' abstract: - lang: eng text: Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait. article_processing_charge: No article_type: original author: - first_name: Anna W. full_name: Santure, Anna W. last_name: Santure - first_name: Isabelle full_name: De Cauwer, Isabelle last_name: De Cauwer - 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: Jocelyn full_name: Poissant, Jocelyn last_name: Poissant - first_name: Ben C. full_name: Sheldon, Ben C. last_name: Sheldon - first_name: Jon full_name: Slate, Jon last_name: Slate citation: ama: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 2013;22(15):3949-3962. doi:10.1111/mec.12376 apa: Santure, A. W., De Cauwer, I., Robinson, M. R., Poissant, J., Sheldon, B. C., & Slate, J. (2013). Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.12376 chicago: Santure, Anna W., Isabelle De Cauwer, Matthew Richard Robinson, Jocelyn Poissant, Ben C. Sheldon, and Jon Slate. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology. Wiley, 2013. https://doi.org/10.1111/mec.12376. ieee: A. W. Santure, I. De Cauwer, M. R. Robinson, J. Poissant, B. C. Sheldon, and J. Slate, “Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population,” Molecular Ecology, vol. 22, no. 15. Wiley, pp. 3949–3962, 2013. ista: Santure AW, De Cauwer I, Robinson MR, Poissant J, Sheldon BC, Slate J. 2013. Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population. Molecular Ecology. 22(15), 3949–3962. mla: Santure, Anna W., et al. “Genomic Dissection of Variation in Clutch Size and Egg Mass in a Wild Great Tit (Parus Major) Population.” Molecular Ecology, vol. 22, no. 15, Wiley, 2013, pp. 3949–62, doi:10.1111/mec.12376. short: A.W. Santure, I. De Cauwer, M.R. Robinson, J. Poissant, B.C. Sheldon, J. Slate, Molecular Ecology 22 (2013) 3949–3962. date_created: 2020-04-30T11:00:32Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T08:15:14Z day: '01' doi: 10.1111/mec.12376 extern: '1' intvolume: ' 22' issue: '15' language: - iso: eng month: '08' oa_version: None page: 3949-3962 publication: Molecular Ecology publication_identifier: issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '7747' abstract: - lang: eng text: Acquisition and allocation of resources are central to life‐history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to partition the genetic basis of multivariate plasticity into independent axes of genetic variation, and quantify for the first time, the extent to which specific traits drive multitrait genotype–environment interactions. Our framework generalises to analyses of plasticity, growth and ageing. We apply this approach to a unique, large‐scale, multivariate study of acquisition, allocation and plasticity in the life history of the cricket, Gryllus firmus. We demonstrate that resource acquisition and allocation are genetically correlated, and that plasticity in trade‐offs between allocation to components of fitness is 90% dependent on genetic variance for total resource acquisition. These results suggest that genotype–environment effects for resource acquisition can maintain variation in life‐history components that are typically observed in the wild. 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: Andrew P. full_name: Beckerman, Andrew P. last_name: Beckerman citation: ama: 'Robinson MR, Beckerman AP. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 2013;16(3):281-290. doi:10.1111/ele.12047' apa: 'Robinson, M. R., & Beckerman, A. P. (2013). Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. Wiley. https://doi.org/10.1111/ele.12047' chicago: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters. Wiley, 2013. https://doi.org/10.1111/ele.12047.' ieee: 'M. R. Robinson and A. P. Beckerman, “Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history,” Ecology Letters, vol. 16, no. 3. Wiley, pp. 281–290, 2013.' ista: 'Robinson MR, Beckerman AP. 2013. Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters. 16(3), 281–290.' mla: 'Robinson, Matthew Richard, and Andrew P. Beckerman. “Quantifying Multivariate Plasticity: Genetic Variation in Resource Acquisition Drives Plasticity in Resource Allocation to Components of Life History.” Ecology Letters, vol. 16, no. 3, Wiley, 2013, pp. 281–90, doi:10.1111/ele.12047.' short: M.R. Robinson, A.P. Beckerman, Ecology Letters 16 (2013) 281–290. date_created: 2020-04-30T11:00:49Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T08:15:15Z day: '01' doi: 10.1111/ele.12047 extern: '1' intvolume: ' 16' issue: '3' language: - iso: eng month: '03' oa_version: None page: 281-290 publication: Ecology Letters publication_identifier: issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2013' ... --- _id: '7775' abstract: - lang: eng text: As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition. article_number: '11000' article_processing_charge: No article_type: original author: - first_name: Samuel S. full_name: Schoenholz, Samuel S. last_name: Schoenholz - 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: Oleg full_name: Kogan, Oleg last_name: Kogan - 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: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d' apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d' chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.' ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.' mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51096d.' short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:58Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51096d extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings II: The transverse length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '7774' abstract: - lang: eng text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*. article_number: '10993' 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: Wouter G. full_name: Ellenbroek, Wouter G. last_name: Ellenbroek - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu citation: ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f' apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51095f' chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.' ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.' mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51095f.' short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:42Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51095f extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings I: The rigidity length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '8030' abstract: - lang: eng text: While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012. article_number: '119' article_processing_charge: No article_type: original author: - 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. C. full_name: Froemke, R. C. last_name: Froemke - first_name: N. full_name: Doyon, N. last_name: Doyon - first_name: M. full_name: Gilson, M. last_name: Gilson - first_name: J. S. full_name: Haas, J. S. last_name: Haas - first_name: R. full_name: Liu, R. last_name: Liu - first_name: A. full_name: Maffei, A. last_name: Maffei - first_name: P. full_name: Miller, P. last_name: Miller - first_name: C. J. full_name: Wierenga, C. J. last_name: Wierenga - first_name: M. A. full_name: Woodin, M. A. last_name: Woodin - first_name: F. full_name: Zenke, F. last_name: Zenke - first_name: H. full_name: Sprekeler, H. last_name: Sprekeler citation: ama: 'Vogels TP, Froemke RC, Doyon N, et al. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 2013;7. doi:10.3389/fncir.2013.00119' apa: 'Vogels, T. P., Froemke, R. C., Doyon, N., Gilson, M., Haas, J. S., Liu, R., … Sprekeler, H. (2013). Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. Frontiers Media. https://doi.org/10.3389/fncir.2013.00119' chicago: 'Vogels, Tim P, R. C. Froemke, N. Doyon, M. Gilson, J. S. Haas, R. Liu, A. Maffei, et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits. Frontiers Media, 2013. https://doi.org/10.3389/fncir.2013.00119.' ieee: 'T. P. Vogels et al., “Inhibitory synaptic plasticity: Spike timing-dependence and putative network function,” Frontiers in Neural Circuits, vol. 7. Frontiers Media, 2013.' ista: 'Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. 2013. Inhibitory synaptic plasticity: Spike timing-dependence and putative network function. Frontiers in Neural Circuits. 7, 119.' mla: 'Vogels, Tim P., et al. “Inhibitory Synaptic Plasticity: Spike Timing-Dependence and Putative Network Function.” Frontiers in Neural Circuits, vol. 7, 119, Frontiers Media, 2013, doi:10.3389/fncir.2013.00119.' short: T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, Frontiers in Neural Circuits 7 (2013). date_created: 2020-06-25T13:23:50Z date_published: 2013-07-18T00:00:00Z date_updated: 2021-01-12T08:16:38Z day: '18' ddc: - '570' doi: 10.3389/fncir.2013.00119 extern: '1' external_id: pmid: - '23882186' file: - access_level: open_access checksum: 9c321cb12977d84048712eefa7f0c497 content_type: application/pdf creator: cziletti date_created: 2020-07-16T11:23:40Z date_updated: 2020-07-16T11:23:40Z file_id: '8123' file_name: 2013_FrontNeurCirc_Vogels.pdf file_size: 1530469 relation: main_file success: 1 file_date_updated: 2020-07-16T11:23:40Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Neural Circuits publication_identifier: eissn: - 1662-5110 publication_status: published publisher: Frontiers Media quality_controlled: '1' status: public title: 'Inhibitory synaptic plasticity: Spike timing-dependence and putative network function' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2013' ... --- _id: '811' abstract: - lang: eng text: Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration. acknowledgement: |- This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release. We thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis. author: - first_name: Anika full_name: Steffen, Anika last_name: Steffen - first_name: Markus full_name: Ladwein, Markus last_name: Ladwein - first_name: Georgi A full_name: Georgi Dimchev id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev - first_name: Anke full_name: Hein, Anke last_name: Hein - first_name: Lisa full_name: Schwenkmezger, Lisa last_name: Schwenkmezger - first_name: Stefan full_name: Arens, Stefan last_name: Arens - first_name: Kathrin full_name: Ladwein, Kathrin I last_name: Ladwein - first_name: J. full_name: Holleboom, J. Margit last_name: Holleboom - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: John full_name: Small, John V last_name: Small - first_name: Janett full_name: Schwarz, Janett last_name: Schwarz - first_name: Ralf full_name: Gerhard, Ralf last_name: Gerhard - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Theresia full_name: Stradal, Theresia E last_name: Stradal - first_name: Cord full_name: Brakebusch, Cord H last_name: Brakebusch - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 2013;126(20):4572-4588. doi:10.1242/jcs.118232 apa: Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens, S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.118232 chicago: Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger, Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.118232. ieee: A. Steffen et al., “Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation,” Journal of Cell Science, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013. ista: Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch C, Rottner K. 2013. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 126(20), 4572–4588. mla: Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” Journal of Cell Science, vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:10.1242/jcs.118232. short: A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens, K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix, T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588. date_created: 2018-12-11T11:48:38Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:16:57Z day: '01' doi: 10.1242/jcs.118232 extern: 1 intvolume: ' 126' issue: '20' month: '01' page: 4572 - 4588 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '6840' quality_controlled: 0 status: public title: Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation 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: 126 year: '2013' ... --- _id: '812' abstract: - lang: eng text: Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes. acknowledgement: "This work was supported in part by Deutsche Forschungsgemeinschaft Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects FWF 1516-B09 and FWF P21292-B09 (to J.V.S.), the Vienna Science and Technology \ Fund (WWTF, to \nJ.V.S. and C.S.), and Australian National Health and \ Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR. Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR. Wedlich-Söldner \ for expression constructs and B. Denker, \nP. Hagendorff, and G. Landsberg for technical assistance." author: - first_name: Stefan full_name: Koestler, Stefan A last_name: Koestler - first_name: Anika full_name: Steffen, Anika last_name: Steffen - first_name: Maria full_name: Maria Nemethova id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Moritz full_name: Winterhoff, Moritz last_name: Winterhoff - first_name: Ningning full_name: Luo, Ningning last_name: Luo - first_name: J. full_name: Holleboom, J. Margit last_name: Holleboom - first_name: Jessica full_name: Krupp, Jessica last_name: Krupp - first_name: Sonja full_name: Jacob, Sonja last_name: Jacob - first_name: Marlene full_name: Vinzenz, Marlene last_name: Vinzenz - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Kai full_name: Schlüter, Kai last_name: Schlüter - first_name: Peter full_name: Gunning, Peter W last_name: Gunning - first_name: Christoph full_name: Winkler, Christoph last_name: Winkler - first_name: Christian full_name: Schmeiser, Christian last_name: Schmeiser - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Theresia full_name: Stradal, Theresia E last_name: Stradal - first_name: John full_name: Small, John V last_name: Small - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 2013;24(18):2861-2875. doi:10.1091/mbc.E12-12-0857 apa: Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. American Society for Biology. https://doi.org/10.1091/mbc.E12-12-0857 chicago: Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell. American Society for Biology, 2013. https://doi.org/10.1091/mbc.E12-12-0857. ieee: S. Koestler et al., “Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin,” Molecular Biology of the Cell, vol. 24, no. 18. American Society for Biology, pp. 2861–2875, 2013. ista: Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C, Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 24(18), 2861–2875. mla: Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” Molecular Biology of the Cell, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75, doi:10.1091/mbc.E12-12-0857. short: S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom, J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler, C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of the Cell 24 (2013) 2861–2875. date_created: 2018-12-11T11:48:38Z date_published: 2013-09-15T00:00:00Z date_updated: 2021-01-12T08:17:00Z day: '15' doi: 10.1091/mbc.E12-12-0857 extern: 1 intvolume: ' 24' issue: '18' month: '09' page: 2861 - 2875 publication: Molecular Biology of the Cell publication_status: published publisher: American Society for Biology publist_id: '6841' quality_controlled: 0 status: public title: Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin type: journal_article volume: 24 year: '2013' ... --- _id: '810' abstract: - lang: eng text: Cryo-electron tomography combined with image processing by sub-tomogram averaging is unique in its power to resolve the structures of proteins and macromolecular complexes in situ. Limitations of the method, including the low signal to noise ratio within individual images from cryo-tomographic datasets and difficulties in determining the defocus at which the data was collected, mean that to date the very best structures obtained by sub-tomogram averaging are limited to a resolution of approximately 15. Å. Here, by optimizing data collection and defocus determination steps, we have determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution alpha-helices can be directly and clearly visualized. These data demonstrate for the first time that high-resolution structural information can be obtained from cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has the potential to allow detailed studies of unsolved and biologically relevant structures under biologically relevant conditions. acknowledgement: The M-PMV ΔPro CANC tubes imaged in this study were a kind gift from Pavel Ulbrich and Tomas Ruml, Institute of Chemical Technology, Prague. The cryo-EM grids were prepared by Tanmay Bharat. This study was technically supported by EMBL’s IT services unit and by Frank Thommen. We thank Martin Schorb and Svetlana Dodonova for discussions and advice; Khanh Huy Bui for advice and scripts to streamline tomogram reconstruction; and Giulia Zanetti, Tanmay Bharat, and Martin Beck for comments on the manuscript. This study was supported by Deutsche Forschungsgemeinschaft grant BR 3635/2-1 to JAGB. author: - first_name: Florian full_name: Florian Schur id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Wim full_name: Hagen, Wim J last_name: Hagen - first_name: Alex full_name: De Marco, Alex last_name: De Marco - first_name: John full_name: Briggs, John A last_name: Briggs citation: ama: Schur FK, Hagen W, De Marco A, Briggs J. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 2013;184(3):394-400. doi:10.1016/j.jsb.2013.10.015 apa: Schur, F. K., Hagen, W., De Marco, A., & Briggs, J. (2013). Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2013.10.015 chicago: Schur, Florian KM, Wim Hagen, Alex De Marco, and John Briggs. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural Biology. Academic Press, 2013. https://doi.org/10.1016/j.jsb.2013.10.015. ieee: F. K. Schur, W. Hagen, A. De Marco, and J. Briggs, “Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging,” Journal of Structural Biology, vol. 184, no. 3. Academic Press, pp. 394–400, 2013. ista: Schur FK, Hagen W, De Marco A, Briggs J. 2013. Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology. 184(3), 394–400. mla: Schur, Florian KM, et al. “Determination of Protein Structure at 8.5Å Resolution Using Cryo-Electron Tomography and Sub-Tomogram Averaging.” Journal of Structural Biology, vol. 184, no. 3, Academic Press, 2013, pp. 394–400, doi:10.1016/j.jsb.2013.10.015. short: F.K. Schur, W. Hagen, A. De Marco, J. Briggs, Journal of Structural Biology 184 (2013) 394–400. date_created: 2018-12-11T11:48:37Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T08:16:54Z day: '01' doi: 10.1016/j.jsb.2013.10.015 extern: 1 intvolume: ' 184' issue: '3' month: '12' page: 394 - 400 publication: Journal of Structural Biology publication_status: published publisher: Academic Press publist_id: '6839' quality_controlled: 0 status: public title: Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging type: journal_article volume: 184 year: '2013' ... --- _id: '8245' abstract: - lang: eng text: "Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS).\r\nResults: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding supports the application of trastuzumab at any stage of the disease." article_number: '307' article_processing_charge: No author: - first_name: Branka full_name: Petricevic, Branka last_name: Petricevic - first_name: Johannes full_name: Laengle, Johannes last_name: Laengle - first_name: Josef full_name: Singer, Josef last_name: Singer - first_name: Monika full_name: Sachet, Monika last_name: Sachet - first_name: Judit full_name: Fazekas, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas orcid: 0000-0002-8777-3502 - first_name: Guenther full_name: Steger, Guenther last_name: Steger - first_name: Rupert full_name: Bartsch, Rupert last_name: Bartsch - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim - first_name: Michael full_name: Bergmann, Michael last_name: Bergmann citation: ama: Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 2013;11. doi:10.1186/1479-5876-11-307 apa: Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G., … Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. Springer Nature. https://doi.org/10.1186/1479-5876-11-307 chicago: Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine. Springer Nature, 2013. https://doi.org/10.1186/1479-5876-11-307. ieee: B. Petricevic et al., “Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients,” Journal of Translational Medicine, vol. 11. Springer Nature, 2013. ista: Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R, Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307. mla: Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” Journal of Translational Medicine, vol. 11, 307, Springer Nature, 2013, doi:10.1186/1479-5876-11-307. short: B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R. Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11 (2013). date_created: 2020-08-10T11:54:34Z date_published: 2013-12-12T00:00:00Z date_updated: 2022-08-25T14:52:39Z day: '12' ddc: - '570' doi: 10.1186/1479-5876-11-307 extern: '1' external_id: pmid: - '24330813' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-10T13:45:19Z date_updated: 2020-08-10T13:45:19Z file_id: '8247' file_name: 2013_JoTM_Petricevic.pdf file_size: 777311 relation: main_file success: 1 file_date_updated: 2020-08-10T13:45:19Z has_accepted_license: '1' intvolume: ' 11' language: - iso: eng month: '12' oa: 1 oa_version: None pmid: 1 publication: Journal of Translational Medicine publication_identifier: issn: - 1479-5876 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2013' ... --- _id: '827' abstract: - lang: eng text: As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed. article_number: '451' author: - first_name: José full_name: O'Brien, José last_name: O'Brien - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00451 apa: O’Brien, J., & Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00451 chicago: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00451. ieee: J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013. ista: O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451. mla: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” Frontiers in Plant Science, vol. 4, 451, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00451. short: J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013). date_created: 2018-12-11T11:48:43Z date_published: 2013-11-19T00:00:00Z date_updated: 2021-01-12T08:17:50Z day: '19' ddc: - '580' department: - _id: EvBe doi: 10.3389/fpls.2013.00451 ec_funded: 1 file: - access_level: open_access checksum: fdc25ddd1bf9a99b99f662cdbafeddd4 content_type: application/pdf creator: dernst date_created: 2019-01-31T10:40:38Z date_updated: 2020-07-14T12:48:11Z file_id: '5903' file_name: 2013_FrontiersPlant_OBrien.pdf file_size: 953299 relation: main_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '6821' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinin cross talking during biotic and abiotic stress responses 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: '2013' ... --- _id: '828' abstract: - lang: eng text: The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed. article_number: '537' author: - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00537 apa: Cuesta, C., Wabnik, K. T., & Benková, E. (2013). Systems approaches to study root architecture dynamics. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00537 chicago: Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00537. ieee: C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research Foundation, 2013. ista: Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537. mla: Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” Frontiers in Plant Science, vol. 4, 537, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00537. short: C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013). date_created: 2018-12-11T11:48:43Z date_published: 2013-12-26T00:00:00Z date_updated: 2021-01-12T08:17:52Z day: '26' ddc: - '580' department: - _id: EvBe doi: 10.3389/fpls.2013.00537 ec_funded: 1 file: - access_level: open_access checksum: 0185b3c4d7df9a94bd3ce5a66d213506 content_type: application/pdf creator: dernst date_created: 2019-01-31T10:36:43Z date_updated: 2020-07-14T12:48:11Z file_id: '5902' file_name: 2013_FrontiersPlant_Cuesta.pdf file_size: 710835 relation: main_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '6820' quality_controlled: '1' scopus_import: 1 status: public title: Systems approaches to study root architecture dynamics 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: '2013' ... --- _id: '830' abstract: - lang: eng text: Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development. acknowledgement: The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript. article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Galbiati, Francesca last_name: Galbiati - first_name: Dola full_name: Sinha Roy, Dola last_name: Sinha Roy - first_name: Sara full_name: Simonini, Sara last_name: Simonini - first_name: Mara full_name: Cucinotta, Mara last_name: Cucinotta - first_name: Luca full_name: Ceccato, Luca last_name: Ceccato - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Mária full_name: Šimášková, Mária last_name: Šimášková - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Yuri full_name: Kamiuchi, Yuri last_name: Kamiuchi - first_name: Mitsuhiro full_name: Aida, Mitsuhiro last_name: Aida - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Rüdiger full_name: Simon, Rüdiger last_name: Simon - first_name: Simona full_name: Masiero, Simona last_name: Masiero - first_name: Lucia full_name: Colombo, Lucia last_name: Colombo citation: ama: Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 2013;76(3):446-455. doi:10.1111/tpj.12309 apa: Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell. https://doi.org/10.1111/tpj.12309 chicago: Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/tpj.12309. ieee: F. Galbiati et al., “An integrative model of the control of ovule primordia formation,” The Plant journal for cell and molecular biology, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013. ista: Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455. mla: Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” The Plant Journal for Cell and Molecular Biology, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:10.1111/tpj.12309. short: F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455. date_created: 2018-12-11T11:48:44Z date_published: 2013-09-19T00:00:00Z date_updated: 2022-03-21T07:17:26Z day: '19' doi: 10.1111/tpj.12309 extern: '1' external_id: pmid: - '23941199' intvolume: ' 76' issue: '3' language: - iso: eng month: '09' oa_version: None page: 446 - 455 pmid: 1 publication: The Plant journal for cell and molecular biology publication_status: published publisher: Wiley-Blackwell publist_id: '6818' quality_controlled: '1' scopus_import: '1' status: public title: An integrative model of the control of ovule primordia formation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 76 year: '2013' ... --- _id: '831' abstract: - lang: eng text: In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes. acknowledgement: This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning. author: - first_name: Benjamin full_name: Péret, Benjamin last_name: Péret - first_name: Alistair full_name: Middleton, Alistair M last_name: Middleton - first_name: Andrew full_name: French, Andrew P last_name: French - first_name: Antoine full_name: Larrieu, Antoine last_name: Larrieu - first_name: Anthony full_name: Bishopp, Anthony last_name: Bishopp - first_name: Maria full_name: Njo, Maria last_name: Njo - first_name: Darren full_name: Wells, Darren M last_name: Wells - first_name: Silvana full_name: Porco, Silvana last_name: Porco - first_name: Nathan full_name: Mellor, Nathan last_name: Mellor - first_name: Leah full_name: Band, Leah R last_name: Band - first_name: Ilda full_name: Casimiro, Ilda last_name: Casimiro - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Ilkka full_name: Sairanen, Ilkka last_name: Sairanen - first_name: Romain full_name: Mallet, Romain last_name: Mallet - first_name: Göran full_name: Sandberg, Göran last_name: Sandberg - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eric full_name: Kramer, Eric last_name: Kramer - first_name: John full_name: King, John R last_name: King - first_name: Ive full_name: De Smet, Ive last_name: De Smet - first_name: Tony full_name: Pridmore, Tony last_name: Pridmore - first_name: Markus full_name: Owen, Markus last_name: Owen - first_name: Malcolm full_name: Bennett, Malcolm J last_name: Bennett citation: ama: Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 2013;9. doi:10.1038/msb.2013.43 apa: Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2013.43 chicago: Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/msb.2013.43. ieee: B. Péret et al., “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” Molecular Systems Biology, vol. 9. Nature Publishing Group, 2013. ista: Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9. mla: Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” Molecular Systems Biology, vol. 9, Nature Publishing Group, 2013, doi:10.1038/msb.2013.43. short: B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013). date_created: 2018-12-11T11:48:44Z date_published: 2013-10-22T00:00:00Z date_updated: 2021-01-12T08:18:03Z day: '22' doi: 10.1038/msb.2013.43 extern: 1 intvolume: ' 9' month: '10' publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '6817' quality_controlled: 0 status: public title: Sequential induction of auxin efflux and influx carriers regulates lateral root emergence 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: 9 year: '2013' ... --- _id: '8461' abstract: - lang: eng text: Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR. article_processing_charge: No article_type: original author: - first_name: Jens D. full_name: Haller, Jens D. last_name: Haller - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 2013;57(3):263-280. doi:10.1007/s10858-013-9787-x' apa: 'Haller, J. D., & Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-013-9787-x' chicago: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR. Springer Nature, 2013. https://doi.org/10.1007/s10858-013-9787-x.' ieee: 'J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” Journal of Biomolecular NMR, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013.' ista: 'Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.' mla: 'Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” Journal of Biomolecular NMR, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:10.1007/s10858-013-9787-x.' short: J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280. date_created: 2020-09-18T10:09:05Z date_published: 2013-10-09T00:00:00Z date_updated: 2021-01-12T08:19:26Z day: '09' doi: 10.1007/s10858-013-9787-x extern: '1' intvolume: ' 57' issue: '3' keyword: - Spectroscopy - Biochemistry language: - iso: eng month: '10' oa_version: None page: 263-280 publication: Journal of Biomolecular NMR publication_identifier: issn: - 0925-2738 - 1573-5001 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2013' ... --- _id: '8462' abstract: - lang: eng text: The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration. article_processing_charge: No article_type: original author: - first_name: E. full_name: Rennella, E. last_name: Rennella - first_name: T. full_name: Cutuil, T. last_name: Cutuil - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: I. full_name: Ayala, I. last_name: Ayala - first_name: F. full_name: Gabel, F. last_name: Gabel - first_name: V. full_name: Forge, V. last_name: Forge - first_name: A. full_name: Corazza, A. last_name: Corazza - first_name: G. full_name: Esposito, G. last_name: Esposito - first_name: B. full_name: Brutscher, B. last_name: Brutscher citation: ama: 'Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 2013;425(15):2722-2736. doi:10.1016/j.jmb.2013.04.028' apa: 'Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2013.04.028' chicago: 'Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology. Elsevier, 2013. https://doi.org/10.1016/j.jmb.2013.04.028.' ieee: 'E. Rennella et al., “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” Journal of Molecular Biology, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.' ista: 'Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.' mla: 'Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” Journal of Molecular Biology, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:10.1016/j.jmb.2013.04.028.' short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736. date_created: 2020-09-18T10:09:12Z date_published: 2013-08-09T00:00:00Z date_updated: 2022-08-25T14:56:24Z day: '09' doi: 10.1016/j.jmb.2013.04.028 extern: '1' intvolume: ' 425' issue: '15' keyword: - Molecular Biology language: - iso: eng month: '08' oa_version: None page: 2722-2736 publication: Journal of Molecular Biology publication_identifier: issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 425 year: '2013' ... --- _id: '899' abstract: - lang: eng text: Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites. author: - first_name: Michael full_name: Breen, Michael S last_name: Breen - first_name: Carsten full_name: Kemena, Carsten last_name: Kemena - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Cédric full_name: Notredame, Cédric last_name: Notredame - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply. Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220 apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013). Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220 chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12220. ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013. ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3. mla: Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220. short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3. date_created: 2018-12-11T11:49:05Z date_published: 2013-05-30T00:00:00Z date_updated: 2021-01-12T08:21:40Z day: '30' doi: 10.1038/nature12220 extern: 1 intvolume: ' 497' issue: '7451' month: '05' page: E2 - E3 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6747' quality_controlled: 0 status: public title: Breen et al. reply type: journal_article volume: 497 year: '2013' ... --- _id: '9674' abstract: - lang: eng text: The coalescence of nano-crystals during sintering is often found to result in interesting crystalline structures such as multi-fold twins, and yet the plasticity mechanism accompanying their formation is unclear. In this work, the sintering behavior of two unsupported copper nanoparticles initially at room temperature is investigated by molecular dynamics simulations under the constant-energy ensemble. The results reveal that once the two nanoparticles are brought into contact, they often go through drastic structural changes with the inter-particle grain boundary quickly eliminated, and single- and multi-fold twinning occurs frequently in the coalesced product. Whereas the formation of single twins is found to be via the more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation of fivefold twins, however, takes place via a novel dislocation-free mechanism involving a series of shear and rigid-body rotation processes caused by elastic waves with amplitudes not corresponding to any allowable Burgers vector in the fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never been reported before. 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: Alfonso H.W. full_name: Ngan, Alfonso H.W. last_name: Ngan citation: ama: 'Cheng B, Ngan AHW. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 2013;47:65-79. doi:10.1016/j.ijplas.2013.01.006' apa: 'Cheng, B., & Ngan, A. H. W. (2013). The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2013.01.006' chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of Plasticity. Elsevier, 2013. https://doi.org/10.1016/j.ijplas.2013.01.006.' ieee: 'B. Cheng and A. H. W. Ngan, “The crystal structures of sintered copper nanoparticles: A molecular dynamics study,” International Journal of Plasticity, vol. 47. Elsevier, pp. 65–79, 2013.' ista: 'Cheng B, Ngan AHW. 2013. The crystal structures of sintered copper nanoparticles: A molecular dynamics study. International Journal of Plasticity. 47, 65–79.' mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Crystal Structures of Sintered Copper Nanoparticles: A Molecular Dynamics Study.” International Journal of Plasticity, vol. 47, Elsevier, 2013, pp. 65–79, doi:10.1016/j.ijplas.2013.01.006.' short: B. Cheng, A.H.W. Ngan, International Journal of Plasticity 47 (2013) 65–79. date_created: 2021-07-15T14:27:44Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T14:04:30Z day: '01' doi: 10.1016/j.ijplas.2013.01.006 extern: '1' intvolume: ' 47' language: - iso: eng month: '08' oa_version: None page: 65-79 publication: International Journal of Plasticity publication_identifier: issn: - 0749-6419 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'The crystal structures of sintered copper nanoparticles: A molecular dynamics study' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 47 year: '2013' ... --- _id: '9676' abstract: - lang: eng text: Despite its relevance to a range of technological applications including nanocrystalline material fabrication, the sintering mechanisms of nanoparticles have not been well understood. It has been recognized that extrapolation from understanding of macro-particle sintering is unreliable for the nano-particle size regime. In this work, the sintering behaviour of copper nanoparticles under periodic boundary conditions at different temperatures and pressures was investigated by Molecular Dynamics simulations. It was found that smaller particle sizes, higher temperature and higher external pressure facilitate densification. Through a comparison with a two-sphere model, the governing mechanisms for many nanoparticles sintered at low temperature (T⩽900K) were identified to be a variety of plasticity processes including dislocation, twinning and even amorphization at the contact neck regions, due to the presence of high stresses. 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: Alfonso H.W. full_name: Ngan, Alfonso H.W. last_name: Ngan citation: ama: 'Cheng B, Ngan AHW. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 2013;74:1-11. doi:10.1016/j.commatsci.2013.03.014' apa: 'Cheng, B., & Ngan, A. H. W. (2013). The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. Elsevier. https://doi.org/10.1016/j.commatsci.2013.03.014' chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational Materials Science. Elsevier, 2013. https://doi.org/10.1016/j.commatsci.2013.03.014.' ieee: 'B. Cheng and A. H. W. Ngan, “The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study,” Computational Materials Science, vol. 74. Elsevier, pp. 1–11, 2013.' ista: 'Cheng B, Ngan AHW. 2013. The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study. Computational Materials Science. 74, 1–11.' mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “The Sintering and Densification Behaviour of Many Copper Nanoparticles: A Molecular Dynamics Study.” Computational Materials Science, vol. 74, Elsevier, 2013, pp. 1–11, doi:10.1016/j.commatsci.2013.03.014.' short: B. Cheng, A.H.W. Ngan, Computational Materials Science 74 (2013) 1–11. date_created: 2021-07-16T06:46:38Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-02-23T14:04:35Z day: '01' doi: 10.1016/j.commatsci.2013.03.014 extern: '1' intvolume: ' 74' language: - iso: eng month: '06' oa_version: None page: 1-11 publication: Computational Materials Science publication_identifier: issn: - 0927-0256 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 74 year: '2013' ... --- _id: '971' abstract: - lang: eng text: We study the stability of the normal state in a mesoscopic NSN junction biased by a constant voltage V with respect to the formation of the superconducting order. Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature dependence of the instability line, V inst(T), where nucleation of superconductivity takes place. For sufficiently low biases, a stationary symmetric superconducting state emerges below the instability line. For higher biases, the normal phase is destroyed by the formation of a nonstationary bimodal state with two superconducting nuclei localized near the opposite terminals. The low-temperature and large-voltage behavior of the instability line is highly sensitive to the details of the inelastic relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T) in NSN junctions may be used as an effective tool to access the parameters of the inelastic relaxation in the normal state. acknowledgement: We are grateful to M. V. Feigel'man, A. Kamenev, T. M. Klapwijk, J. P. Pekola, V. V. Ryazanov, J. C. W. Song, and D. Y. Vodolazov for discussions. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Mikhail full_name: Skvortsov, Mikhail A last_name: Skvortsov citation: ama: Serbyn M, Skvortsov M. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. 2013;87(2). doi:10.1103/PhysRevB.87.020501 apa: Serbyn, M., & Skvortsov, M. (2013). Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.020501 chicago: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.020501. ieee: M. Serbyn and M. Skvortsov, “Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 2. American Physical Society, 2013. ista: Serbyn M, Skvortsov M. 2013. Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge. Physical Review B - Condensed Matter and Materials Physics. 87(2). mla: Serbyn, Maksym, and Mikhail Skvortsov. “Onset of Superconductivity in a Voltage-Biased Normal-Superconducting-Normal Microbridge.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.87.020501. short: M. Serbyn, M. Skvortsov, Physical Review B - Condensed Matter and Materials Physics 87 (2013). date_created: 2018-12-11T11:49:28Z date_published: 2013-01-02T00:00:00Z date_updated: 2021-01-12T08:22:20Z day: '02' doi: 10.1103/PhysRevB.87.020501 extern: 1 intvolume: ' 87' issue: '2' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1208.6004 month: '01' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6429' quality_controlled: 0 status: public title: Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge type: journal_article volume: 87 year: '2013' ... --- _id: '972' abstract: - lang: eng text: In topological crystalline insulators (TCIs), topology and crystal symmetry intertwine to create surface states with distinct characteristics. The breaking of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac fermions. Here, we report high-resolution scanning tunneling microscopy studies of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected by crystal symmetry with massive Dirac fermions consistent with crystal symmetry breaking. In addition, we show two distinct regimes of the Fermi surface topology separated by a Van-Hove singularity at the Lifshitz transition point. Our work paves the way for engineering the Dirac band gap and realizing interaction-driven topological quantum phenomena in TCIs. author: - first_name: Yoshinori full_name: Okada, Yoshinori last_name: Okada - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Hsin full_name: Lin, Hsin last_name: Lin - first_name: Daniel full_name: Walkup, Daniel last_name: Walkup - first_name: Wenwen full_name: Zhou, Wenwen last_name: Zhou - first_name: Chetan full_name: Dhital, Chetan last_name: Dhital - first_name: Madhab full_name: Neupane, Madhab last_name: Neupane - first_name: Suyang full_name: Xu, Suyang last_name: Xu - first_name: Yungjui full_name: Wang, Yungjui last_name: Wang - first_name: Raman full_name: Sankar, Raman last_name: Sankar - first_name: Fangcheng full_name: Chou, Fangcheng last_name: Chou - first_name: Arun full_name: Bansil, Arun last_name: Bansil - first_name: Md full_name: Hasan, Md last_name: Hasan - first_name: Stephen full_name: Wilson, Stephen last_name: Wilson - first_name: Liang full_name: Fu, Liang last_name: Fu - first_name: Vidya full_name: Madhavan, Vidya last_name: Madhavan citation: ama: Okada Y, Serbyn M, Lin H, et al. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. 2013;341(6153):1496-1499. doi:10.1126/science.1239451 apa: Okada, Y., Serbyn, M., Lin, H., Walkup, D., Zhou, W., Dhital, C., … Madhavan, V. (2013). Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1239451 chicago: Okada, Yoshinori, Maksym Serbyn, Hsin Lin, Daniel Walkup, Wenwen Zhou, Chetan Dhital, Madhab Neupane, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1239451. ieee: Y. Okada et al., “Observation of dirac node formation and mass acquisition in a topological crystalline insulator,” Science, vol. 341, no. 6153. American Association for the Advancement of Science, pp. 1496–1499, 2013. ista: Okada Y, Serbyn M, Lin H, Walkup D, Zhou W, Dhital C, Neupane M, Xu S, Wang Y, Sankar R, Chou F, Bansil A, Hasan M, Wilson S, Fu L, Madhavan V. 2013. Observation of dirac node formation and mass acquisition in a topological crystalline insulator. Science. 341(6153), 1496–1499. mla: Okada, Yoshinori, et al. “Observation of Dirac Node Formation and Mass Acquisition in a Topological Crystalline Insulator.” Science, vol. 341, no. 6153, American Association for the Advancement of Science, 2013, pp. 1496–99, doi:10.1126/science.1239451. short: Y. Okada, M. Serbyn, H. Lin, D. Walkup, W. Zhou, C. Dhital, M. Neupane, S. Xu, Y. Wang, R. Sankar, F. Chou, A. Bansil, M. Hasan, S. Wilson, L. Fu, V. Madhavan, Science 341 (2013) 1496–1499. date_created: 2018-12-11T11:49:29Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:22:20Z day: '01' doi: 10.1126/science.1239451 extern: '1' external_id: arxiv: - '1305.2823' intvolume: ' 341' issue: '6153' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1305.2823 month: '01' oa: 1 oa_version: Preprint page: 1496 - 1499 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '6430' quality_controlled: '1' status: public title: Observation of dirac node formation and mass acquisition in a topological crystalline insulator type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 341 year: '2013' ... --- _id: '975' abstract: - lang: eng text: Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic in time, growth of the entanglement entropy for initial product states in a putative many-body localized phase. We show that this surprising phenomenon results from the dephasing due to exponentially small interaction-induced corrections to the eigenenergies of different states. For weak interactions, we find that the entanglement entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the single-particle localization length. The saturated value of the entanglement entropy at long times is determined by the participation ratios of the initial state over the eigenstates of the subsystem. Our work shows that the logarithmic entanglement growth is a universal phenomenon characteristic of the many-body localized phase in any number of spatial dimensions, and reveals a broad hierarchy of dephasing time scales present in such a phase. acknowledgement: We would like to thank E. Altman and J. Moore for useful comments on the manuscript. This research was supported in part by Perimeter Institute for Theoretical Physics. 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. Z. P. was supported by DOE Grant No. DE-SC0002140. The simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University. 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. Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. 2013;110(26). doi:10.1103/PhysRevLett.110.260601 apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.260601 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.260601. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Universal slow growth of entanglement in interacting strongly disordered systems,” Physical Review Letters, vol. 110, no. 26. American Physical Society, 2013. ista: Serbyn M, Papić Z, Abanin D. 2013. Universal slow growth of entanglement in interacting strongly disordered systems. Physical Review Letters. 110(26). mla: Serbyn, Maksym, et al. “Universal Slow Growth of Entanglement in Interacting Strongly Disordered Systems.” Physical Review Letters, vol. 110, no. 26, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.260601. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:49:29Z date_published: 2013-06-28T00:00:00Z date_updated: 2021-01-12T08:22:22Z day: '28' doi: 10.1103/PhysRevLett.110.260601 extern: 1 intvolume: ' 110' issue: '26' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1304.4605 month: '06' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6426' quality_controlled: 0 status: public title: Universal slow growth of entanglement in interacting strongly disordered systems type: journal_article volume: 110 year: '2013' ... --- _id: '9749' abstract: - lang: eng text: Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise. article_processing_charge: No author: - first_name: Benjamin full_name: Zagorsky, Benjamin last_name: Zagorsky - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:10.1371/journal.pone.0080814.s001 apa: Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. https://doi.org/10.1371/journal.pone.0080814.s001 chicago: Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0080814.s001. ieee: B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013. ista: Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, 10.1371/journal.pone.0080814.s001. mla: Zagorsky, Benjamin, et al. Forgiver Triumphs in Alternating Prisoner’s Dilemma . Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.s001. short: B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013). date_created: 2021-07-28T15:45:07Z date_published: 2013-12-12T00:00:00Z date_updated: 2023-02-23T10:34:39Z day: '12' department: - _id: KrCh doi: 10.1371/journal.pone.0080814.s001 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '2247' relation: used_in_publication status: public status: public title: 'Forgiver triumphs in alternating prisoner''s dilemma ' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2013' ... --- _id: '2944' abstract: - lang: eng text: 'We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.' acknowledged_ssus: - _id: ScienComp acknowledgement: This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13). author: - first_name: Simon full_name: Aeschbacher, Simon id: 2D35326E-F248-11E8-B48F-1D18A9856A87 last_name: Aeschbacher - first_name: Andreas full_name: Futschik, Andreas last_name: Futschik - first_name: Mark full_name: Beaumont, Mark last_name: Beaumont citation: ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165' apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165' chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/mec.12165.' ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.' ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.' mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” Molecular Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.' short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002. date_created: 2018-12-11T12:00:28Z date_published: 2013-02-01T00:00:00Z date_updated: 2023-02-23T14:07:19Z day: '01' department: - _id: NiBa doi: 10.1111/mec.12165 intvolume: ' 22' issue: '4' language: - iso: eng month: '02' oa_version: None page: 987 - 1002 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '3788' quality_controlled: '1' related_material: record: - id: '9758' relation: research_data status: public scopus_import: 1 status: public title: 'Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2013' ... --- _id: '894' abstract: - lang: eng text: 'Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.' acknowledgement: Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320. author: - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Arkhipov, Vladimir last_name: Arkhipov - first_name: Hélène full_name: Corbel, Hélène last_name: Corbel - first_name: Adrien full_name: Frantz, Adrien last_name: Frantz - first_name: Julien full_name: Gasparini, Julien last_name: Gasparini - first_name: Lisa full_name: Jacquin, Lisa last_name: Jacquin - first_name: Gwenaël full_name: Jacob, Gwenaël last_name: Jacob - first_name: Sophie full_name: Thibault, Sophie last_name: Thibault - first_name: Emmanuelle full_name: Baudry, Emmanuelle last_name: Baudry citation: ama: Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1). doi:10.1186/1756-0500-6-310 apa: Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310 chicago: Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310. ieee: R. Derelle et al., “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1. BioMed Central, 2013. ista: Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1). mla: Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central, 2013, doi:10.1186/1756-0500-6-310. short: R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013). date_created: 2018-12-11T11:49:04Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:21:25Z day: '01' doi: 10.1186/1756-0500-6-310 extern: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa_version: None publication: BMC Research Notes publication_status: published publisher: BioMed Central publist_id: '6752' status: public title: Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2013' ... --- _id: '9055' abstract: - lang: eng text: Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional "living crystals," which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles. article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: S. full_name: Sacanna, S. last_name: Sacanna - first_name: A. P. full_name: Steinberg, A. P. last_name: Steinberg - first_name: D. J. full_name: Pine, D. J. last_name: Pine - first_name: P. M. full_name: Chaikin, P. M. last_name: Chaikin citation: ama: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of light-activated colloidal surfers. Science. 2013;339(6122):936-940. doi:10.1126/science.1230020 apa: Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., & Chaikin, P. M. (2013). Living crystals of light-activated colloidal surfers. Science. American Association for the Advancement of Science . https://doi.org/10.1126/science.1230020 chicago: Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” Science. American Association for the Advancement of Science , 2013. https://doi.org/10.1126/science.1230020. ieee: J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin, “Living crystals of light-activated colloidal surfers,” Science, vol. 339, no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013. ista: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals of light-activated colloidal surfers. Science. 339(6122), 936–940. mla: Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.” Science, vol. 339, no. 6122, American Association for the Advancement of Science , 2013, pp. 936–40, doi:10.1126/science.1230020. short: J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science 339 (2013) 936–940. date_created: 2021-02-01T14:37:29Z date_published: 2013-02-22T00:00:00Z date_updated: 2022-08-25T14:57:43Z day: '22' doi: 10.1126/science.1230020 extern: '1' external_id: pmid: - '23371555' intvolume: ' 339' issue: '6122' keyword: - Multidisciplinary language: - iso: eng month: '02' oa_version: None page: 936-940 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: 'American Association for the Advancement of Science ' quality_controlled: '1' scopus_import: '1' status: public title: Living crystals of light-activated colloidal surfers type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2013' ... --- _id: '905' abstract: - lang: eng text: A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia. acknowledgement: We thank Natalya Kveten and Oksana Makarova, heads of administrations of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions. Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological literature. We are very grateful to The David and Lucile Packard Foundation for the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011 and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation team in Russia. author: - first_name: Vladimir full_name: Arkhipov, Vladimir Y last_name: Arkhipov - first_name: T full_name: Noah T last_name: Noah - first_name: Steffen full_name: Koschkar, Steffen last_name: Koschkar - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. 2013;(29):25-30. apa: Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club. chicago: Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club, 2013. ieee: V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30, 2013. ista: Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30. mla: Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30. short: V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30. date_created: 2018-12-11T11:49:07Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:21:48Z day: '01' extern: 1 issue: '29' main_file_link: - open_access: '1' url: http://orientalbirdclub.org/forktail29/ month: '09' oa: 1 page: 25 - 30 publication: Forktail publication_status: published publisher: Oriental Bird Club publist_id: '6741' quality_controlled: 0 status: public title: Birds of Mys Shmidta, north Chukotka, Russia type: journal_article year: '2013' ... --- _id: '9153' abstract: - lang: eng text: Internal tide driven mixing plays a key role in sustaining the deep ocean stratification and meridional overturning circulation. Internal tides can be generated by topographic horizontal scales ranging from hundreds of meters to tens of kilometers. State of the art topographic products barely resolve scales smaller than ∼10 km in the deep ocean. On these scales abyssal hills dominate ocean floor roughness. The impact of abyssal hill roughness on internal‐tide generation is evaluated in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated based on linear wave theory both in real and spectral space using the Shuttle Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution with and without the addition of synthetic abyssal hill roughness. Internal tide generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the energy flux due to larger topographic scales resolved in standard products in both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean ridges, where abyssal hill roughness is large. Focusing on two regions located over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally linear theory predicts an increase of the energy flux due to abyssal hills of up to 100% or 60% when an empirical correction for supercritical slopes is attempted. Therefore, abyssal hills, unresolved in state of the art topographic products, can have a strong impact on internal tide generation, especially over mid‐ocean ridges. article_processing_charge: No article_type: original author: - first_name: Angélique full_name: Melet, Angélique last_name: Melet - first_name: Maxim full_name: Nikurashin, Maxim last_name: Nikurashin - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: S. full_name: Falahat, S. last_name: Falahat - first_name: Jonas full_name: Nycander, Jonas last_name: Nycander - first_name: Patrick G. full_name: Timko, Patrick G. last_name: Timko - first_name: Brian K. full_name: Arbic, Brian K. last_name: Arbic - first_name: John A. full_name: Goff, John A. last_name: Goff citation: ama: 'Melet A, Nikurashin M, Muller CJ, et al. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 2013;118(11):6303-6318. doi:10.1002/2013jc009212' apa: 'Melet, A., Nikurashin, M., Muller, C. J., Falahat, S., Nycander, J., Timko, P. G., … Goff, J. A. (2013). Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2013jc009212' chicago: 'Melet, Angélique, Maxim Nikurashin, Caroline J Muller, S. Falahat, Jonas Nycander, Patrick G. Timko, Brian K. Arbic, and John A. Goff. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2013. https://doi.org/10.1002/2013jc009212.' ieee: 'A. Melet et al., “Internal tide generation by abyssal hills using analytical theory,” Journal of Geophysical Research: Oceans, vol. 118, no. 11. American Geophysical Union, pp. 6303–6318, 2013.' ista: 'Melet A, Nikurashin M, Muller CJ, Falahat S, Nycander J, Timko PG, Arbic BK, Goff JA. 2013. Internal tide generation by abyssal hills using analytical theory. Journal of Geophysical Research: Oceans. 118(11), 6303–6318.' mla: 'Melet, Angélique, et al. “Internal Tide Generation by Abyssal Hills Using Analytical Theory.” Journal of Geophysical Research: Oceans, vol. 118, no. 11, American Geophysical Union, 2013, pp. 6303–18, doi:10.1002/2013jc009212.' short: 'A. Melet, M. Nikurashin, C.J. Muller, S. Falahat, J. Nycander, P.G. Timko, B.K. Arbic, J.A. Goff, Journal of Geophysical Research: Oceans 118 (2013) 6303–6318.' date_created: 2021-02-15T15:11:39Z date_published: 2013-11-07T00:00:00Z date_updated: 2022-01-24T13:46:15Z day: '07' doi: 10.1002/2013jc009212 extern: '1' intvolume: ' 118' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/2013JC009212 month: '11' oa: 1 oa_version: Published Version page: 6303-6318 publication: 'Journal of Geophysical Research: Oceans' publication_identifier: issn: - 2169-9275 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: Internal tide generation by abyssal hills using analytical theory type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 118 year: '2013' ... --- _id: '9154' abstract: - lang: eng text: "In this study the response of tropical precipitation extremes to warming in organized convection is examined using a cloud-resolving model. Vertical shear is imposed to organize the convection into squall lines. Earlier studies show that in disorganized convection, the fractional increase of precipitation extremes is similar to that of surface water vapor, which is substantially smaller than the increase in column water vapor. It has been suggested that organized convection could lead to stronger amplifications.\r\nRegardless of the strength of the shear, amplifications of precipitation extremes in the cloud-resolving simulations are comparable to those of surface water vapor and are substantially less than increases in column water vapor. The results without shear and with critical shear, for which the squall lines are perpendicular to the shear, are surprisingly similar with a fractional rate of increase of precipitation extremes slightly smaller than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic, and stronger supercritical shear yields larger rates, close to or slightly larger than surface humidity.\r\nA scaling is used to evaluate the thermodynamic and dynamic contributions to precipitation extreme changes. To first order, they are dominated by the thermodynamic component, which has the same magnitude for all shears, close to the change in surface water vapor. The dynamic contribution plays a secondary role and tends to weaken extremes without shear and with critical shear, while it strengthens extremes with supercritical shear. These different dynamic contributions for different shears are due to different responses of convective mass fluxes in individual updrafts to warming." article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: ama: Muller CJ. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 2013;26(14):5028-5043. doi:10.1175/jcli-d-12-00655.1 apa: Muller, C. J. (2013). Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. American Meteorological Society. https://doi.org/10.1175/jcli-d-12-00655.1 chicago: Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate. American Meteorological Society, 2013. https://doi.org/10.1175/jcli-d-12-00655.1. ieee: C. J. Muller, “Impact of convective organization on the response of tropical precipitation extremes to warming,” Journal of Climate, vol. 26, no. 14. American Meteorological Society, pp. 5028–5043, 2013. ista: Muller CJ. 2013. Impact of convective organization on the response of tropical precipitation extremes to warming. Journal of Climate. 26(14), 5028–5043. mla: Muller, Caroline J. “Impact of Convective Organization on the Response of Tropical Precipitation Extremes to Warming.” Journal of Climate, vol. 26, no. 14, American Meteorological Society, 2013, pp. 5028–43, doi:10.1175/jcli-d-12-00655.1. short: C.J. Muller, Journal of Climate 26 (2013) 5028–5043. date_created: 2021-02-15T15:26:39Z date_published: 2013-07-15T00:00:00Z date_updated: 2022-01-24T13:46:41Z day: '15' doi: 10.1175/jcli-d-12-00655.1 extern: '1' intvolume: ' 26' issue: '14' keyword: - Atmospheric Science language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1175/JCLI-D-12-00655.1 month: '07' oa: 1 oa_version: Published Version page: 5028-5043 publication: Journal of Climate publication_identifier: issn: - 0894-8755 - 1520-0442 publication_status: published publisher: American Meteorological Society quality_controlled: '1' status: public title: Impact of convective organization on the response of tropical precipitation extremes to warming type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 26 year: '2013' ... --- _id: '9167' abstract: - lang: eng text: We introduce a self-propelled colloidal hematite docker that can be steered to a small particle cargo many times its size, dock, transport the cargo to a remote location, and then release it. The self-propulsion and docking are reversible and activated by visible light. The docker can be steered either by a weak uniform magnetic field or by nanoscale tracks in a textured substrate. The light-activated motion and docking originate from osmotic/phoretic particle transport in a concentration gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of the hematite. The docking mechanism is versatile and can be applied to various materials and shapes. The hematite dockers are simple single-component particles and are synthesized in bulk quantities. This system opens up new possibilities for designing complex micrometer-size factories as well as new biomimetic systems. article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: Adrian full_name: Vatchinsky, Adrian last_name: Vatchinsky - first_name: Paul M. full_name: Chaikin, Paul M. last_name: Chaikin - first_name: David J. full_name: Pine, David J. last_name: Pine citation: ama: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 2013;135(43):15978-15981. doi:10.1021/ja406090s apa: Palacci, J. A., Sacanna, S., Vatchinsky, A., Chaikin, P. M., & Pine, D. J. (2013). Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja406090s chicago: Palacci, Jérémie A, Stefano Sacanna, Adrian Vatchinsky, Paul M. Chaikin, and David J. Pine. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society. American Chemical Society, 2013. https://doi.org/10.1021/ja406090s. ieee: J. A. Palacci, S. Sacanna, A. Vatchinsky, P. M. Chaikin, and D. J. Pine, “Photoactivated colloidal dockers for cargo transportation,” Journal of the American Chemical Society, vol. 135, no. 43. American Chemical Society, pp. 15978–15981, 2013. ista: Palacci JA, Sacanna S, Vatchinsky A, Chaikin PM, Pine DJ. 2013. Photoactivated colloidal dockers for cargo transportation. Journal of the American Chemical Society. 135(43), 15978–15981. mla: Palacci, Jérémie A., et al. “Photoactivated Colloidal Dockers for Cargo Transportation.” Journal of the American Chemical Society, vol. 135, no. 43, American Chemical Society, 2013, pp. 15978–81, doi:10.1021/ja406090s. short: J.A. Palacci, S. Sacanna, A. Vatchinsky, P.M. Chaikin, D.J. Pine, Journal of the American Chemical Society 135 (2013) 15978–15981. date_created: 2021-02-18T14:31:26Z date_published: 2013-10-30T00:00:00Z date_updated: 2021-02-22T10:10:41Z day: '30' doi: 10.1021/ja406090s extern: '1' external_id: arxiv: - '1310.5724' pmid: - '24131488' intvolume: ' 135' issue: '43' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1310.5724 month: '10' oa: 1 oa_version: Preprint page: 15978-15981 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - '15205126' issn: - '00027863' publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Photoactivated colloidal dockers for cargo transportation type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 135 year: '2013' ... --- _id: '921' abstract: - lang: eng text: Recent experiments have shown that spreading epithelial sheets exhibit a long-range coordination of motility forces that leads to a buildup of tension in the tissue, which may enhance cell division and the speed of wound healing. Furthermore, the edges of these epithelial sheets commonly show finger-like protrusions whereas the bulk often displays spontaneous swirls of motile cells. To explain these experimental observations, we propose a simple flocking-type mechanism, in which cells tend to align their motility forceswith their velocity. Implementing this idea in amechanical tissue simulation, the proposed model gives rise to efficient spreading and can explain the experimentally observed long-range alignment of motility forces in highly disordered patterns, as well as the buildup of tensile stress throughout the tissue. Our model also qualitatively reproduces the dependence of swirl size and swirl velocity on cell density reported in experiments and exhibits an undulation instability at the edge of the spreading tissue commonly observed in vivo. Finally, we study the dependence of colony spreading speed on important physical and biological parameters and derive simple scaling relations that show that coordination of motility forces leads to an improvement of the wound healing process for realistic tissue parameters. acknowledgement: "This work was supported by National Science Foundation (NSF) Grant DMS-1068869 and by the NSF Center for Theoretical Biological Physics (Grant NSF PHY-0822283).\r\nWe acknowledge useful discussions with Eshel Ben-Jacob and Assaf Zaritsky. " article_processing_charge: No author: - first_name: Markus full_name: Basan, Markus last_name: Basan - first_name: Jens full_name: Elgeti, Jens last_name: Elgeti - 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: Wouter full_name: Rappel, Wouter last_name: Rappel - first_name: Herbert full_name: Levine, Herbert last_name: Levine citation: ama: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 2013;110(7):2452-2459. doi:10.1073/pnas.1219937110 apa: Basan, M., Elgeti, J., Hannezo, E. B., Rappel, W., & Levine, H. (2013). Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219937110 chicago: Basan, Markus, Jens Elgeti, Edouard B Hannezo, Wouter Rappel, and Herbert Levine. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219937110. ieee: M. Basan, J. Elgeti, E. B. Hannezo, W. Rappel, and H. Levine, “Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2452–2459, 2013. ista: Basan M, Elgeti J, Hannezo EB, Rappel W, Levine H. 2013. Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing. PNAS. 110(7), 2452–2459. mla: Basan, Markus, et al. “Alignment of Cellular Motility Forces with Tissue Flow as a Mechanism for Efficient Wound Healing.” PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2452–59, doi:10.1073/pnas.1219937110. short: M. Basan, J. Elgeti, E.B. Hannezo, W. Rappel, H. Levine, PNAS 110 (2013) 2452–2459. date_created: 2018-12-11T11:49:12Z date_published: 2013-02-12T00:00:00Z date_updated: 2021-01-12T08:21:55Z day: '12' doi: 10.1073/pnas.1219937110 extern: '1' intvolume: ' 110' issue: '7' language: - iso: eng month: '02' oa_version: None page: 2452 - 2459 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6518' status: public title: Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '9459' abstract: - lang: eng text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway. article_processing_charge: No article_type: original author: - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Ping-Hung full_name: Hsieh, Ping-Hung last_name: Hsieh - first_name: Devin full_name: Coleman-Derr, Devin last_name: Coleman-Derr - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Ka full_name: Thao, Ka last_name: Thao - first_name: Stacey L. full_name: Harmer, Stacey L. last_name: Harmer - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033 apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.02.033 chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033. ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” Cell, vol. 153, no. 1. Elsevier, pp. 193–205, 2013. ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205. mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033. short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205. date_created: 2021-06-04T12:23:28Z date_published: 2013-03-28T00:00:00Z date_updated: 2021-12-14T08:25:35Z day: '28' department: - _id: DaZi doi: 10.1016/j.cell.2013.02.033 extern: '1' external_id: pmid: - '23540698' intvolume: ' 153' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2013.02.033 month: '03' oa: 1 oa_version: Published Version page: 193-205 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 153 year: '2013' ... --- _id: '9481' abstract: - lang: eng text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants. article_processing_charge: No article_type: original author: - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Randy full_name: Ruan, Randy last_name: Ruan - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Manoj K. full_name: Sharma, Manoj K. last_name: Sharma - first_name: Rita full_name: Sharma, Rita last_name: Sharma - first_name: Pamela C full_name: Ronald, Pamela C last_name: Ronald - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939. doi:10.1073/pnas.1306164110 apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1306164110 chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110. ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013. ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939. mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110. short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939. date_created: 2021-06-07T07:31:02Z date_published: 2013-05-07T00:00:00Z date_updated: 2021-12-14T08:26:44Z day: '07' department: - _id: DaZi doi: 10.1073/pnas.1306164110 extern: '1' external_id: pmid: - '23613580' intvolume: ' 110' issue: '19' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1306164110 month: '05' oa: 1 oa_version: Published Version page: 7934-7939 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 110 year: '2013' ... --- _id: '9663' abstract: - lang: eng text: 'Molecular dynamics simulations of small Cu nanoparticles using three different interatomic potentials at rising temperature indicate that small nanoparticles can undergo solid-solid structural transitions through a direct geometrical conversion route. The direct geometrical conversion can happen for cuboctahedral nanoparticles, which turn into an icosahedra shape: one diagonal of the square faces contracts, and the faces are folded along the diagonal to give rise to two equilateral triangles. The transition is a kinetic process that cannot be fully explained through an energetic point of view. It has low activation energy and fast reaction time in the simulations. The transition mechanism is via the transmission of shear waves initiated from the particle surface and does not involve dislocation activity.' article_number: '164314' 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: Alfonso H. W. full_name: Ngan, Alfonso H. W. last_name: Ngan citation: ama: Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 2013;138(16). doi:10.1063/1.4802025 apa: Cheng, B., & Ngan, A. H. W. (2013). Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4802025 chicago: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The Journal of Chemical Physics. AIP Publishing, 2013. https://doi.org/10.1063/1.4802025. ieee: B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion,” The Journal of Chemical Physics, vol. 138, no. 16. AIP Publishing, 2013. ista: Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 138(16), 164314. mla: Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” The Journal of Chemical Physics, vol. 138, no. 16, 164314, AIP Publishing, 2013, doi:10.1063/1.4802025. short: B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013). date_created: 2021-07-15T09:27:58Z date_published: 2013-04-28T00:00:00Z date_updated: 2021-08-09T12:35:34Z day: '28' doi: 10.1063/1.4802025 extern: '1' external_id: pmid: - '23635145' intvolume: ' 138' issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://pubmed.ncbi.nlm.nih.gov/23635145/ month: '04' oa: 1 oa_version: Submitted Version pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 138 year: '2013' ... --- _id: '9682' abstract: - lang: eng text: In this work, we simulate the response of two Cu nanoparticles colliding at different approaching rates at room temperature by MD. For small nanospheres, the formation of single twins is favored at high approach rates, whereas larger nanospheres mainly deform by dislocation slip. For small nanocubes with large {100} flat surfaces, however, a dislocation-free direct geometrical conversion process that leads to five-fold twinning dominates except at highly retarded approaching rates. For larger nanocubes, single twin formation is the governing plasticity mechanism. The probability for plastic deformation by dislocation slip or twinning is attributed to the abundance of surface steps, which act as sites for dislocation nucleation. 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: Alfonso H.W. full_name: Ngan, Alfonso H.W. last_name: Ngan citation: ama: 'Cheng B, Ngan AHW. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 2013;585:326-334. doi:10.1016/j.msea.2013.07.065' apa: 'Cheng, B., & Ngan, A. H. W. (2013). Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. Elsevier. https://doi.org/10.1016/j.msea.2013.07.065' chicago: 'Cheng, Bingqing, and Alfonso H.W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” Materials Science and Engineering: A. Elsevier, 2013. https://doi.org/10.1016/j.msea.2013.07.065.' ieee: 'B. Cheng and A. H. W. Ngan, “Crystal plasticity of Cu nanocrystals during collision,” Materials Science and Engineering: A, vol. 585. Elsevier, pp. 326–334, 2013.' ista: 'Cheng B, Ngan AHW. 2013. Crystal plasticity of Cu nanocrystals during collision. Materials Science and Engineering: A. 585, 326–334.' mla: 'Cheng, Bingqing, and Alfonso H. W. Ngan. “Crystal Plasticity of Cu Nanocrystals during Collision.” Materials Science and Engineering: A, vol. 585, Elsevier, 2013, pp. 326–34, doi:10.1016/j.msea.2013.07.065.' short: 'B. Cheng, A.H.W. Ngan, Materials Science and Engineering: A 585 (2013) 326–334.' date_created: 2021-07-19T09:04:36Z date_published: 2013-11-15T00:00:00Z date_updated: 2023-02-23T14:04:51Z day: '15' doi: 10.1016/j.msea.2013.07.065 extern: '1' intvolume: ' 585' language: - iso: eng month: '11' oa_version: None page: 326-334 publication: 'Materials Science and Engineering: A' publication_identifier: issn: - 0921-5093 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Crystal plasticity of Cu nanocrystals during collision type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 585 year: '2013' ... --- _id: '970' abstract: - lang: eng text: 'Recently a new high-mobility Dirac material, trilayer graphene, was realized experimentally. The band structure of ABA-stacked trilayer graphene consists of a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties of ABA-stacked trilayer graphene biased by a perpendicular electric field. We find that the combination of the bias and trigonal warping gives rise to a set of new Dirac points: In each valley, seven species of Dirac fermions with small masses of order of a few meV emerge. The positions and masses of the emergent Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity at the neutrality point is expected to show nonmonotonic behavior, becoming of the order of a few e2/h when some Dirac masses vanish. Further, we analyze the evolution of the Landau level spectrum as a function of bias. The emergence of new Dirac points in the band structure translates into new threefold-degenerate groups of Landau levels. This leads to an anomalous quantum Hall effect, in which some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies of all Landau levels get lifted, and in this regime all quantum Hall plateaus are spaced by e2/h. Finally, we show that the pattern of Landau level crossings is very sensitive to certain band structure parameters, and can therefore provide a useful tool for determining their precise values.' acknowledgement: We thank Pablo Jarillo-Herrero, Leonardo Campos, and Thiti Taychatanapat for attracting our attention to the problem of biased trilayer graphene, and for many helpful discussions. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Dmitry full_name: Abanin, Dmitry A last_name: Abanin citation: ama: Serbyn M, Abanin D. New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. 2013;87(11). doi:10.1103/PhysRevB.87.115422 apa: Serbyn, M., & Abanin, D. (2013). New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.87.115422 chicago: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.87.115422. ieee: M. Serbyn and D. Abanin, “New Dirac points and multiple Landau level crossings in biased trilayer graphene,” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 11. American Physical Society, 2013. ista: Serbyn M, Abanin D. 2013. New Dirac points and multiple Landau level crossings in biased trilayer graphene. Physical Review B - Condensed Matter and Materials Physics. 87(11). mla: Serbyn, Maksym, and Dmitry Abanin. “New Dirac Points and Multiple Landau Level Crossings in Biased Trilayer Graphene.” Physical Review B - Condensed Matter and Materials Physics, vol. 87, no. 11, American Physical Society, 2013, doi:10.1103/PhysRevB.87.115422. short: M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 87 (2013). date_created: 2018-12-11T11:49:28Z date_published: 2013-03-18T00:00:00Z date_updated: 2021-01-12T08:22:20Z day: '18' doi: 10.1103/PhysRevB.87.115422 extern: 1 intvolume: ' 87' issue: '11' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1212.6251 month: '03' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6428' quality_controlled: 0 status: public title: New Dirac points and multiple Landau level crossings in biased trilayer graphene type: journal_article volume: 87 year: '2013' ... --- _id: '973' abstract: - lang: eng text: We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion. acknowledgement: We thank J. Moore for useful discussions. 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. Z. P. was supported by DOE Grant No. DE-SC0002140. M. S. was supported by the National Science Foundation under Grant No. DMR-1104498. The simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University. 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. Local conservation laws and the structure of the many body localized states. Physical Review Letters. 2013;111(12). doi:10.1103/PhysRevLett.111.127201 apa: Serbyn, M., Papić, Z., & Abanin, D. (2013). Local conservation laws and the structure of the many body localized states. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.111.127201 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Local Conservation Laws and the Structure of the Many Body Localized States.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.111.127201. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Local conservation laws and the structure of the many body localized states,” Physical Review Letters, vol. 111, no. 12. American Physical Society, 2013. ista: Serbyn M, Papić Z, Abanin D. 2013. Local conservation laws and the structure of the many body localized states. Physical Review Letters. 111(12). mla: Serbyn, Maksym, et al. “Local Conservation Laws and the Structure of the Many Body Localized States.” Physical Review Letters, vol. 111, no. 12, American Physical Society, 2013, doi:10.1103/PhysRevLett.111.127201. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review Letters 111 (2013). date_created: 2018-12-11T11:49:29Z date_published: 2013-09-17T00:00:00Z date_updated: 2021-01-12T08:22:21Z day: '17' doi: 10.1103/PhysRevLett.111.127201 extern: 1 intvolume: ' 111' issue: '12' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1305.5554 month: '09' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6424' quality_controlled: 0 status: public title: Local conservation laws and the structure of the many body localized states type: journal_article volume: 111 year: '2013' ... --- _id: '974' abstract: - lang: eng text: We propose a possible realization of the overscreened Kondo impurity problem by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid fixed point in the overscreened Kondo problem. Using a large-N expansion together with an expansion in the dynamical exponent of the gauge field, we find that the coupling to the gauge field leads to weak but observable changes in the physical properties of the system at the overscreened Kondo fixed point. We discuss the extrapolation of this result to a physical case and argue that the realization of overscreened Kondo physics could lead to observations of effects due to gauge fields. author: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Senthil T, Lee P. Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. 2013;88(2). doi:10.1103/PhysRevB.88.024419 apa: Serbyn, M., Senthil, T., & Lee, P. (2013). Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.88.024419 chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.024419. ieee: M. Serbyn, T. Senthil, and P. Lee, “Overscreened Kondo fixed point in S=1 spin liquid,” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 2. American Physical Society, 2013. ista: Serbyn M, Senthil T, Lee P. 2013. Overscreened Kondo fixed point in S=1 spin liquid. Physical Review B - Condensed Matter and Materials Physics. 88(2). mla: Serbyn, Maksym, et al. “Overscreened Kondo Fixed Point in S=1 Spin Liquid.” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 2, American Physical Society, 2013, doi:10.1103/PhysRevB.88.024419. short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 88 (2013). date_created: 2018-12-11T11:49:29Z date_published: 2013-07-19T00:00:00Z date_updated: 2021-01-12T08:22:21Z day: '19' doi: 10.1103/PhysRevB.88.024419 extern: '1' external_id: arxiv: - '1212.5179' intvolume: ' 88' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1212.5179 month: '07' oa: 1 oa_version: Preprint publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6425' quality_controlled: '1' status: public title: Overscreened Kondo fixed point in S=1 spin liquid type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 88 year: '2013' ... --- _id: '2284' abstract: - lang: eng text: 'Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal-originally described for honeybees as "hygienic behaviour"-is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.' acknowledgement: "The study was funded by the European Research Council (Marie Curie ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n" article_number: '225' author: - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Michel full_name: Chapuisat, Michel last_name: Chapuisat - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 2013;13(1). doi:10.1186/1471-2148-13-225 apa: Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., & Cremer, S. (2013). Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-225 chicago: Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-225. ieee: S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013. ista: Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 13(1), 225. mla: Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” BMC Evolutionary Biology, vol. 13, no. 1, 225, BioMed Central, 2013, doi:10.1186/1471-2148-13-225. short: S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary Biology 13 (2013). date_created: 2018-12-11T11:56:46Z date_published: 2013-10-14T00:00:00Z date_updated: 2023-02-23T14:07:06Z day: '14' ddc: - '570' department: - _id: SyCr doi: 10.1186/1471-2148-13-225 ec_funded: 1 file: - access_level: open_access checksum: c16ef36f2a10786a7885e19c4528d707 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:41Z date_updated: 2020-07-14T12:45:37Z file_id: '5026' file_name: IST-2016-402-v1+1_1471-2148-13-225.pdf file_size: 281736 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '4647' pubrep_id: '402' quality_controlled: '1' related_material: record: - id: '9753' relation: research_data status: public scopus_import: 1 status: public title: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2013' ... --- _id: '2277' abstract: - lang: eng text: Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible. article_number: e1003344 author: - first_name: Kristina full_name: Simmons, Kristina last_name: Simmons - first_name: Jason full_name: Prentice, Jason last_name: Prentice - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Jan full_name: Homann, Jan last_name: Homann - first_name: Heather full_name: Yee, Heather last_name: Yee - first_name: Stephanie full_name: Palmer, Stephanie last_name: Palmer - first_name: Philip full_name: Nelson, Philip last_name: Nelson - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian citation: ama: Simmons K, Prentice J, Tkačik G, et al. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003344 apa: Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2013). Transformation of stimulus correlations by the retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003344 chicago: Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003344. ieee: K. Simmons et al., “Transformation of stimulus correlations by the retina,” PLoS Computational Biology, vol. 9, no. 12. Public Library of Science, 2013. ista: Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2013. Transformation of stimulus correlations by the retina. PLoS Computational Biology. 9(12), e1003344. mla: Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344. short: K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, PLoS Computational Biology 9 (2013). date_created: 2018-12-11T11:56:43Z date_published: 2013-12-05T00:00:00Z date_updated: 2023-02-23T14:07:04Z day: '05' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1003344 file: - access_level: open_access checksum: 46722afc4f7eabb0831165d9c1b171ad content_type: application/pdf creator: system date_created: 2018-12-12T10:14:36Z date_updated: 2020-07-14T12:45:36Z file_id: '5089' file_name: IST-2016-410-v1+1_journal.pcbi.1003344.pdf file_size: 3115568 relation: main_file file_date_updated: 2020-07-14T12:45:36Z has_accepted_license: '1' intvolume: ' 9' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '4667' pubrep_id: '410' quality_controlled: '1' related_material: record: - id: '9752' relation: research_data status: public scopus_import: 1 status: public title: Transformation of stimulus correlations by the retina 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: 9 year: '2013' ...